{"lab": {"uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "Z2lsYmVydEBzZGJyaS5vcmc=", "@id": "/users/1dbb8e49-38e4-4154-a97c-af8176a58c44/", "display_title": "David Gilbert"}], "display_title": "David Gilbert, SDBRI", "title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "award": {"@id": "/awards/1U54DK107965-01/", "description": "NOFIC: Decades of microscopy have revealed that the nucleus is not a homogeneous organelle, but rather consists of distinct compartments such as nucleoli, nuclear speckles, the nuclear lamina, among other structures. Increasing evidence indicates that specific genomic regions each associate with these compartments. This genome compartmentalization has been linked to various functions, but these links are still poorly understood. Interestingly, Lamina Associated Domains (LADs) share specific heterochromatin marks, defining chromatin domains with distinct genetic and epigenetic properties. Genomic regions associating with other nuclear compartments may similarly define distinct classes of chromatin domains. One major bottleneck towards a deeper understanding of nuclear organization has been the inability to convert microscopy views of nuclear compartments into genome-wide maps that show which loci are associated with which compartment, and how the chromosomal fiber traverses between compartments. In addition, there is an urgent need for more efficient methods to dissect the mechanisms by which large genomic regions are targeted to specific nuclear compartments. Finally, there is an urgent need for high-throughput approaches that query the functional relevance of genome compartmentalization. For this Center grant, we propose to meet these needs through the following Aims: 1. Develop a strategy that connects microscopy views to genome-wide maps that, together with modeling, reveal the localization and dynamics of genomic regions relative to all major nuclear compartments. 2. Develop methods for efficient manipulation of the genome in order to elucidate mechanisms that target loci to specific compartments. 3. Develop methods to measure, model, and validate the functional relevance of nuclear compartments. The combined results of these approaches will reveal causal relationships now hidden among entangled genomic, epigenetic, and nuclear organization features. Deliverables of this proposal include a wide range of structural and functional maps of nuclear organization, reagents for visualizing endogenous chromosome loci, a powerful pipeline for synthesis of ~100kb DNA fragments, and cell lines facilitating repeated, high-fidelity insertio of these large fragments back into selected sites in the genome. These resources will provide a powerful complement to other 4D Nucleome Consortium efforts. A key strength of this Center proposal is the experience and complementary research capabilities of its five Investigators. Together they will pool their expertise for a concerted investigation into the biological functions of nuclear compartmentalization.", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "name": "1U54DK107965-01", "center_title": "NOFIC - Belmont", "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "status": "current", "@type": ["Award", "Item"], "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["gilbert-lab:h1_16_phase_repliseq_bioreplicates"], "accession": "4DNESXRBILXJ", "condition": "All fractions", "description": "16 fraction Repliseq and G1 fraction on H1-hESC Tier 1 cells", "date_created": "2019-03-21T20:42:11.433411+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "16-fraction Repli-seq on H1-hESC", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-10-04T20:04:39.710424+00:00"}, "public_release": "2021-10-13", "schema_version": "2", "static_headers": [{"lab": {"display_title": "David Gilbert, SDBRI", "@id": "/labs/david-gilbert-lab/", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "body": "This experiment set supercedes [4DNESL48CTGR](https://data.4dnucleome.org/experiment-set-replicates/bc80bbf7-a2b9-4866-90ed-b9c1e7951be4/) because a new biological replicate was added.", "name": "static-header.replacing_item_4DNESXRBILXJ", "award": {"@type": ["Award", "Item"], "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "status": "current", "@id": "/awards/1U54DK107965-01/", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Note: Replaced Item - 4DNESXRBILXJ", "status": "released", "aliases": ["static_header:replacing_item_4DNESXRBILXJ_old_4DNESL48CTGR"], "options": {"filetype": "md", "title_icon": "info", "collapsible": false, "default_open": true}, "date_created": "2019-04-03T19:51:33.881383+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-11-12T14:18:22.353921+00:00"}, "schema_version": "2", "@id": "/static-sections/df7469fd-8074-4e17-8c2a-c179f80e924c/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "df7469fd-8074-4e17-8c2a-c179f80e924c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}, "display_title": "Note: Replaced Item - 4DNESXRBILXJ", "external_references": [], "content": "This experiment set supercedes [4DNESL48CTGR](https://data.4dnucleome.org/experiment-set-replicates/bc80bbf7-a2b9-4866-90ed-b9c1e7951be4/) because a new biological replicate was added.", "filetype": "md", "content_as_html": "

This experiment set supercedes 4DNESL48CTGR because a new biological replicate was added.

"}], "project_release": "2019-04-03", "experiments_in_set": [{"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P5 - 4DNEXXYBNRD1", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "43d1e344-457b-4d3c-95d5-e527651fc6ea", "accession": "4DNEXXYBNRD1", "files": [{"uuid": "b2c84511-0eea-4a6f-b01f-3c5a1708d46a", "accession": "4DNFIWWBJXNA", "file_classification": "raw file", "display_title": "4DNFIWWBJXNA.fastq.gz", "file_size": 1668650158, "href": "/files-fastq/4DNFIWWBJXNA/@@download/4DNFIWWBJXNA.fastq.gz", "md5sum": "568e36f593dc987a5f88ce1440cf6907", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b2c84511-0eea-4a6f-b01f-3c5a1708d46a/4DNFIWWBJXNA.fastq.gz", "@id": "/files-fastq/4DNFIWWBJXNA/", "upload_key": "b2c84511-0eea-4a6f-b01f-3c5a1708d46a/4DNFIWWBJXNA.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWWBJXNA/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 34367637, "uuid": "b2f9cf18-39a6-4d5a-9973-f098d9e57617", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/b2f9cf18-39a6-4d5a-9973-f098d9e57617/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P5 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P05", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXXYBNRD1/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIAIK8KMO.bam", "upload_key": "ca4df2a9-349e-48a3-8a42-f78b81937588/4DNFIAIK8KMO.bam", "href": "/files-processed/4DNFIAIK8KMO/@@download/4DNFIAIK8KMO.bam", "accession": "4DNFIAIK8KMO", "md5sum": "19f1ceeb83f9efff39fb3978d17b47b6", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIAIK8KMO/", "file_size": 1501442591, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ca4df2a9-349e-48a3-8a42-f78b81937588/4DNFIAIK8KMO.bam", "file_type_detailed": "alignments (bam)", "uuid": "ca4df2a9-349e-48a3-8a42-f78b81937588", "status": "released", "quality_metric": {"status": "released", "uuid": "228b868f-db38-4d69-a2d4-57456da057b6", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/228b868f-db38-4d69-a2d4-57456da057b6/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "28366034", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.397", "tooltip": "Percent of total aligned reads (=1.25m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:58.578508+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P5 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P05", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIYH6REBI.bedGraph.gz", "upload_key": "4f49e270-7e6b-44dd-8d04-647fe8cf7116/4DNFIYH6REBI.bedGraph.gz", "href": "/files-processed/4DNFIYH6REBI/@@download/4DNFIYH6REBI.bedGraph.gz", "accession": "4DNFIYH6REBI", "md5sum": "19c275e871f9d07e228e2b9dd97b3860", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'HUcbO-BYRRWSFOMIgdGZDw'", "@id": "/files-processed/4DNFIYH6REBI/", "file_size": 3942039, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4f49e270-7e6b-44dd-8d04-647fe8cf7116/4DNFIYH6REBI.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "4f49e270-7e6b-44dd-8d04-647fe8cf7116", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIYH6REBI - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P5 of 16 fractions", "@id": "/higlass-view-configs/4673fe36-1a4e-4e50-8103-d6af518b74d2/", "uuid": "4673fe36-1a4e-4e50-8103-d6af518b74d2", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "5c5350d36525f21d732b4a68863e796a", "file_size": 1017465, "href": "/files-processed/4DNFIYH6REBI/@@download/4DNFIYH6REBI.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "882ab8fcb6e0435777f1ce2752d51220", "file_size": 4498165, "href": "/files-processed/4DNFIYH6REBI/@@download/4DNFIYH6REBI.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:53.184455+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P5 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P05", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P5 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P5 of 16 fractions", "value": "P5 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:54.962778+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P11 - 4DNEXZPBA82F", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "fcf143b6-740c-440d-8abf-7aaa47519017", "accession": "4DNEXZPBA82F", "files": [{"uuid": "71104c0f-639b-452d-97bd-fa4eadd5c9fc", "accession": "4DNFI8UOHVLP", "file_classification": "raw file", "display_title": "4DNFI8UOHVLP.fastq.gz", "file_size": 2107897700, "href": "/files-fastq/4DNFI8UOHVLP/@@download/4DNFI8UOHVLP.fastq.gz", "md5sum": "087effdb51c080bcd30542d6beed55ca", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/71104c0f-639b-452d-97bd-fa4eadd5c9fc/4DNFI8UOHVLP.fastq.gz", "@id": "/files-fastq/4DNFI8UOHVLP/", "upload_key": "71104c0f-639b-452d-97bd-fa4eadd5c9fc/4DNFI8UOHVLP.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8UOHVLP/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 43543986, "uuid": "1bb3f4cc-b071-45ba-917c-c6bdb23932d1", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/1bb3f4cc-b071-45ba-917c-c6bdb23932d1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P11 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P11", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXZPBA82F/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIPOU7VFY.bam", "upload_key": "32619e07-a092-4711-9124-8f3c4efce816/4DNFIPOU7VFY.bam", "href": "/files-processed/4DNFIPOU7VFY/@@download/4DNFIPOU7VFY.bam", "accession": "4DNFIPOU7VFY", "md5sum": "5e89bfcf471f75f3f17cb8c5ead42c3b", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIPOU7VFY/", "file_size": 1886027808, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/32619e07-a092-4711-9124-8f3c4efce816/4DNFIPOU7VFY.bam", "file_type_detailed": "alignments (bam)", "uuid": "32619e07-a092-4711-9124-8f3c4efce816", "status": "released", "quality_metric": {"status": "released", "uuid": "b6b9feb0-1b67-4c7a-9125-9ed1fe641add", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/b6b9feb0-1b67-4c7a-9125-9ed1fe641add/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "36339107", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.617", "tooltip": "Percent of total aligned reads (=1.68m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:41:16.661265+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P11 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P11", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIVIAWJRK.bedGraph.gz", "upload_key": "3ecf8d06-bc29-4aeb-a3af-d0b0c51360cd/4DNFIVIAWJRK.bedGraph.gz", "href": "/files-processed/4DNFIVIAWJRK/@@download/4DNFIVIAWJRK.bedGraph.gz", "accession": "4DNFIVIAWJRK", "md5sum": "04d3fc1e0c047367981faa56eae71f5c", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "CnUMFcpORfq1dIuV8WVyRg", "@id": "/files-processed/4DNFIVIAWJRK/", "file_size": 4070915, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3ecf8d06-bc29-4aeb-a3af-d0b0c51360cd/4DNFIVIAWJRK.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "3ecf8d06-bc29-4aeb-a3af-d0b0c51360cd", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIVIAWJRK - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P11 of 16 fractions", "@id": "/higlass-view-configs/1a43dddb-37fc-43cc-871d-e98fe01fb6ac/", "uuid": "1a43dddb-37fc-43cc-871d-e98fe01fb6ac", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "d74899c28cdaf07f77c47e774c6047e3", "file_size": 1018221, "href": "/files-processed/4DNFIVIAWJRK/@@download/4DNFIVIAWJRK.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"href": "/files-processed/4DNFIVIAWJRK/@@download/4DNFIVIAWJRK.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:48.496630+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P11 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P11", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P11 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P11 of 16 fractions", "value": "P11 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:17.188723+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P14 - 4DNEXXIXTTXI", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "a92f050e-5b6c-4e7f-bb6b-693b951a0bcc", "accession": "4DNEXXIXTTXI", "files": [{"uuid": "40676f29-877a-42fd-837a-827cbcca4300", "accession": "4DNFIDY6C91T", "file_classification": "raw file", "display_title": "4DNFIDY6C91T.fastq.gz", "file_size": 1247889481, "href": "/files-fastq/4DNFIDY6C91T/@@download/4DNFIDY6C91T.fastq.gz", "md5sum": "2b2f4313f762ae8c51fa1e65bec7bf48", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/40676f29-877a-42fd-837a-827cbcca4300/4DNFIDY6C91T.fastq.gz", "@id": "/files-fastq/4DNFIDY6C91T/", "upload_key": "40676f29-877a-42fd-837a-827cbcca4300/4DNFIDY6C91T.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDY6C91T/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 25864672, "uuid": "2a550392-ee3a-43d6-ac14-ec77ede40237", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/2a550392-ee3a-43d6-ac14-ec77ede40237/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P14 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P14", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXXIXTTXI/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI79HUNBK.bam", "upload_key": "28c43c23-36d3-4431-a986-8cafeb8a147a/4DNFI79HUNBK.bam", "href": "/files-processed/4DNFI79HUNBK/@@download/4DNFI79HUNBK.bam", "accession": "4DNFI79HUNBK", "md5sum": "343ba6ac2d7691fcaa45b2361a23e621", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI79HUNBK/", "file_size": 1012160733, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/28c43c23-36d3-4431-a986-8cafeb8a147a/4DNFI79HUNBK.bam", "file_type_detailed": "alignments (bam)", "uuid": "28c43c23-36d3-4431-a986-8cafeb8a147a", "status": "released", "quality_metric": {"status": "released", "uuid": "1e62c3cb-f739-4674-9aa4-333a697136cc", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/1e62c3cb-f739-4674-9aa4-333a697136cc/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "19227278", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.596", "tooltip": "Percent of total aligned reads (=0.88m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:56.550322+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P14 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P14", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI3WGTLPN.bedGraph.gz", "upload_key": "e37e0c84-4309-4a68-b1ae-d9a59641262b/4DNFI3WGTLPN.bedGraph.gz", "href": "/files-processed/4DNFI3WGTLPN/@@download/4DNFI3WGTLPN.bedGraph.gz", "accession": "4DNFI3WGTLPN", "md5sum": "9a4bc0763b1a786b465d304032f714ef", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "BwT4A54rR6q1goPo1MFagg", "@id": "/files-processed/4DNFI3WGTLPN/", "file_size": 3828801, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e37e0c84-4309-4a68-b1ae-d9a59641262b/4DNFI3WGTLPN.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "e37e0c84-4309-4a68-b1ae-d9a59641262b", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI3WGTLPN - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P14 of 16 fractions", "@id": "/higlass-view-configs/ae53ce99-0679-4025-b1c1-90b0ef730334/", "uuid": "ae53ce99-0679-4025-b1c1-90b0ef730334", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "3248d6171a22102fe0a4cf924d538144", "file_size": 1017936, "href": "/files-processed/4DNFI3WGTLPN/@@download/4DNFI3WGTLPN.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "a03c940db63cd9151f118a5032dbcd8b", "file_size": 4368502, "href": "/files-processed/4DNFI3WGTLPN/@@download/4DNFI3WGTLPN.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:52.709935+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P14 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P14", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P14 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P14 of 16 fractions", "value": "P14 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:13.820658+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P2 - 4DNEXSK4XA98", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "a98aeeda-b640-4768-8878-8a17b9965024", "accession": "4DNEXSK4XA98", "files": [{"uuid": "e4c88fe5-768f-4048-b816-90963f57e892", "accession": "4DNFI4FFL2S3", "file_classification": "raw file", "display_title": "4DNFI4FFL2S3.fastq.gz", "file_size": 1183624049, "href": "/files-fastq/4DNFI4FFL2S3/@@download/4DNFI4FFL2S3.fastq.gz", "md5sum": "e57af285b9a02545ba99b163645dbdeb", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e4c88fe5-768f-4048-b816-90963f57e892/4DNFI4FFL2S3.fastq.gz", "@id": "/files-fastq/4DNFI4FFL2S3/", "upload_key": "e4c88fe5-768f-4048-b816-90963f57e892/4DNFI4FFL2S3.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4FFL2S3/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 24376398, "uuid": "dc1b14d9-1eeb-4c4e-b3e0-03b8d99ecd28", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/dc1b14d9-1eeb-4c4e-b3e0-03b8d99ecd28/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P2 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P02", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXSK4XA98/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFISTVEOCY.bam", "upload_key": "c850d9ce-c935-49f0-ab45-8f6a730a48f1/4DNFISTVEOCY.bam", "href": "/files-processed/4DNFISTVEOCY/@@download/4DNFISTVEOCY.bam", "accession": "4DNFISTVEOCY", "md5sum": "96c418f77fb44d8a7542cb7edd464de4", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISTVEOCY/", "file_size": 1004439887, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c850d9ce-c935-49f0-ab45-8f6a730a48f1/4DNFISTVEOCY.bam", "file_type_detailed": "alignments (bam)", "uuid": "c850d9ce-c935-49f0-ab45-8f6a730a48f1", "status": "released", "quality_metric": {"status": "released", "uuid": "42586192-579f-4e31-b577-0b562cf670ab", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/42586192-579f-4e31-b577-0b562cf670ab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "19583609", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "7.383", "tooltip": "Percent of total aligned reads (=1.45m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:06.169397+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P2 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P02", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI25WQDGU.bedGraph.gz", "upload_key": "c04f9933-f89d-4340-9cd4-e6ce4327e7bc/4DNFI25WQDGU.bedGraph.gz", "href": "/files-processed/4DNFI25WQDGU/@@download/4DNFI25WQDGU.bedGraph.gz", "accession": "4DNFI25WQDGU", "md5sum": "77f90c332cd5ad8af6c855d59f6a5822", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'FXU2nfbkQtO5Q13Tyc9Kag'", "@id": "/files-processed/4DNFI25WQDGU/", "file_size": 3843141, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c04f9933-f89d-4340-9cd4-e6ce4327e7bc/4DNFI25WQDGU.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "c04f9933-f89d-4340-9cd4-e6ce4327e7bc", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI25WQDGU - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P2 of 16 fractions", "@id": "/higlass-view-configs/8b68095e-29ef-469e-a8bf-e8e18f052a01/", "uuid": "8b68095e-29ef-469e-a8bf-e8e18f052a01", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "b7f34a4d5bac280357fdd5dc26bccfd6", "file_size": 1017282, "href": "/files-processed/4DNFI25WQDGU/@@download/4DNFI25WQDGU.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "06bc395b2d43a41df07c1ddfe9f339ef", "file_size": 4404443, "href": "/files-processed/4DNFI25WQDGU/@@download/4DNFI25WQDGU.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:57.127959+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P2 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P02", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P2 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P2 of 16 fractions", "value": "P2 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:51.601954+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P16 - 4DNEX28OSAGW", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "9fa622cf-72c6-4725-8e54-f34bea6fe9d0", "accession": "4DNEX28OSAGW", "files": [{"uuid": "9001f181-617b-4f47-a5f2-f332ae680624", "accession": "4DNFISW6TIRR", "file_classification": "raw file", "display_title": "4DNFISW6TIRR.fastq.gz", "file_size": 1396193476, "href": "/files-fastq/4DNFISW6TIRR/@@download/4DNFISW6TIRR.fastq.gz", "md5sum": "463786de4d23fb7b5f9dec4d09e22c9b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9001f181-617b-4f47-a5f2-f332ae680624/4DNFISW6TIRR.fastq.gz", "@id": "/files-fastq/4DNFISW6TIRR/", "upload_key": "9001f181-617b-4f47-a5f2-f332ae680624/4DNFISW6TIRR.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISW6TIRR/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 29172420, "uuid": "fa272929-8b90-41e1-9807-fec1a6fcd6bf", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/fa272929-8b90-41e1-9807-fec1a6fcd6bf/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P16 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P16", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX28OSAGW/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIU7OAWNV.bam", "upload_key": "7f0563cc-9ded-4510-8397-b27efce08308/4DNFIU7OAWNV.bam", "href": "/files-processed/4DNFIU7OAWNV/@@download/4DNFIU7OAWNV.bam", "accession": "4DNFIU7OAWNV", "md5sum": "61f4813b1c3f473f0e252e6921c40ba6", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIU7OAWNV/", "file_size": 1014117401, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7f0563cc-9ded-4510-8397-b27efce08308/4DNFIU7OAWNV.bam", "file_type_detailed": "alignments (bam)", "uuid": "7f0563cc-9ded-4510-8397-b27efce08308", "status": "released", "quality_metric": {"status": "released", "uuid": "0d0d7e13-6b18-405e-8067-4f9f35dba255", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/0d0d7e13-6b18-405e-8067-4f9f35dba255/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "19968562", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "8.657", "tooltip": "Percent of total aligned reads (=1.73m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:41:49.986465+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P16 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P16", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFITMC3M4S.bedGraph.gz", "upload_key": "3ef2ae0c-5864-48d4-a956-6f113937d4be/4DNFITMC3M4S.bedGraph.gz", "href": "/files-processed/4DNFITMC3M4S/@@download/4DNFITMC3M4S.bedGraph.gz", "accession": "4DNFITMC3M4S", "md5sum": "c6da765e1a6bc0d74d649c80a1dfd869", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'N_RO_LmJQ5eHqUJ4RkNAhw'", "@id": "/files-processed/4DNFITMC3M4S/", "file_size": 3767506, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3ef2ae0c-5864-48d4-a956-6f113937d4be/4DNFITMC3M4S.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "3ef2ae0c-5864-48d4-a956-6f113937d4be", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFITMC3M4S - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P16 of 16 fractions", "@id": "/higlass-view-configs/d6f22a5d-90f9-453a-8522-1d130ee87d22/", "uuid": "d6f22a5d-90f9-453a-8522-1d130ee87d22", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "cfb66fe8a1f0dfc549a655bb3b75d80b", "file_size": 1011057, "href": "/files-processed/4DNFITMC3M4S/@@download/4DNFITMC3M4S.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "8b402d3a722e65e105f2344874984527", "file_size": 4360577, "href": "/files-processed/4DNFITMC3M4S/@@download/4DNFITMC3M4S.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:38.337541+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P16 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P16", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P16 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P16 of 16 fractions", "value": "P16 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:07.810798+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P3 - 4DNEXKCP8338", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "f43e24e1-da36-4ac9-a42f-5f9abebec876", "accession": "4DNEXKCP8338", "files": [{"uuid": "0eb33032-8a67-4c5d-8d82-97df3dd3bd6a", "accession": "4DNFIAYKT1PH", "file_classification": "raw file", "display_title": "4DNFIAYKT1PH.fastq.gz", "file_size": 1284240590, "href": "/files-fastq/4DNFIAYKT1PH/@@download/4DNFIAYKT1PH.fastq.gz", "md5sum": "15f1427ad4c674b0e5a334cda0d39d25", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0eb33032-8a67-4c5d-8d82-97df3dd3bd6a/4DNFIAYKT1PH.fastq.gz", "@id": "/files-fastq/4DNFIAYKT1PH/", "upload_key": "0eb33032-8a67-4c5d-8d82-97df3dd3bd6a/4DNFIAYKT1PH.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAYKT1PH/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 25849381, "uuid": "0a9dd017-ac72-4bab-ab68-b70edc53ee86", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/0a9dd017-ac72-4bab-ab68-b70edc53ee86/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P3 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P03", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXKCP8338/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFITPBC44Z.bam", "upload_key": "921eced5-6ca0-44e0-8ec1-e4f17142bd4e/4DNFITPBC44Z.bam", "href": "/files-processed/4DNFITPBC44Z/@@download/4DNFITPBC44Z.bam", "accession": "4DNFITPBC44Z", "md5sum": "8b005065fa0f7ddeff0569e1518e684e", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFITPBC44Z/", "file_size": 1136445070, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/921eced5-6ca0-44e0-8ec1-e4f17142bd4e/4DNFITPBC44Z.bam", "file_type_detailed": "alignments (bam)", "uuid": "921eced5-6ca0-44e0-8ec1-e4f17142bd4e", "status": "released", "quality_metric": {"status": "released", "uuid": "de3a2caa-87a3-48e4-81f9-5726be9e2e7b", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/de3a2caa-87a3-48e4-81f9-5726be9e2e7b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "21398104", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.896", "tooltip": "Percent of total aligned reads (=1.05m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:45:16.380720+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P3 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P03", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI66HSEY1.bedGraph.gz", "upload_key": "80a3c259-b1ea-4b6e-9ea3-71979bd73f26/4DNFI66HSEY1.bedGraph.gz", "href": "/files-processed/4DNFI66HSEY1/@@download/4DNFI66HSEY1.bedGraph.gz", "accession": "4DNFI66HSEY1", "md5sum": "3c64f3beb28d9136e5081f655f3f6ffd", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "UdrY-H8TTP21mwD-25VTew", "@id": "/files-processed/4DNFI66HSEY1/", "file_size": 3871476, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/80a3c259-b1ea-4b6e-9ea3-71979bd73f26/4DNFI66HSEY1.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "80a3c259-b1ea-4b6e-9ea3-71979bd73f26", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI66HSEY1 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P3 of 16 fractions", "@id": "/higlass-view-configs/bf0b091e-8791-4b9d-96af-c16310a8b800/", "uuid": "bf0b091e-8791-4b9d-96af-c16310a8b800", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "b03bde2074fddb20213b1772e3e59f53", "file_size": 1018593, "href": "/files-processed/4DNFI66HSEY1/@@download/4DNFI66HSEY1.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "7935d27396ec26cb743357f0e94709ca", "file_size": 4388516, "href": "/files-processed/4DNFI66HSEY1/@@download/4DNFI66HSEY1.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:37.238478+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P3 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P03", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P3 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P3 of 16 fractions", "value": "P3 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:25.712671+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P9 - 4DNEX7T7A9QP", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "1fc7e9f9-b6db-4985-b658-d0edca6e3106", "accession": "4DNEX7T7A9QP", "files": [{"uuid": "3f18bd79-ab1c-4a0b-9ea1-be276cb5e16f", "accession": "4DNFIAS7G87G", "file_classification": "raw file", "display_title": "4DNFIAS7G87G.fastq.gz", "file_size": 934453627, "href": "/files-fastq/4DNFIAS7G87G/@@download/4DNFIAS7G87G.fastq.gz", "md5sum": "c42061f96fbdb9bdfd5a615f5bf898bc", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3f18bd79-ab1c-4a0b-9ea1-be276cb5e16f/4DNFIAS7G87G.fastq.gz", "@id": "/files-fastq/4DNFIAS7G87G/", "upload_key": "3f18bd79-ab1c-4a0b-9ea1-be276cb5e16f/4DNFIAS7G87G.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAS7G87G/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 18202791, "uuid": "9fba60fd-f58d-488e-97e1-c4f040371a37", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/9fba60fd-f58d-488e-97e1-c4f040371a37/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P9 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P09", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX7T7A9QP/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI8MTWG8X.bam", "upload_key": "3572826d-21d0-4977-b7f9-a4589e11f740/4DNFI8MTWG8X.bam", "href": "/files-processed/4DNFI8MTWG8X/@@download/4DNFI8MTWG8X.bam", "accession": "4DNFI8MTWG8X", "md5sum": "03238313ad8f71a8687bf245d3f55c2d", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI8MTWG8X/", "file_size": 894892513, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3572826d-21d0-4977-b7f9-a4589e11f740/4DNFI8MTWG8X.bam", "file_type_detailed": "alignments (bam)", "uuid": "3572826d-21d0-4977-b7f9-a4589e11f740", "status": "released", "quality_metric": {"status": "released", "uuid": "14698c1d-a2a1-4d48-a54d-2e1868b02de2", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/14698c1d-a2a1-4d48-a54d-2e1868b02de2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "15487679", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "2.299", "tooltip": "Percent of total aligned reads (=0.36m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:30.533929+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P9 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P09", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIE36RMQE.bedGraph.gz", "upload_key": "9e58ed26-26f6-42c7-ab78-4791d4b0e311/4DNFIE36RMQE.bedGraph.gz", "href": "/files-processed/4DNFIE36RMQE/@@download/4DNFIE36RMQE.bedGraph.gz", "accession": "4DNFIE36RMQE", "md5sum": "e11a756b16aca5dbd21ec7836dea9cc3", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'FXEjYmdjRvy6bpzFT301xQ'", "@id": "/files-processed/4DNFIE36RMQE/", "file_size": 3806320, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9e58ed26-26f6-42c7-ab78-4791d4b0e311/4DNFIE36RMQE.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "9e58ed26-26f6-42c7-ab78-4791d4b0e311", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIE36RMQE - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P9 of 16 fractions", "@id": "/higlass-view-configs/dacb65a3-ed3f-4d56-8375-e8f3ac3efe0f/", "uuid": "dacb65a3-ed3f-4d56-8375-e8f3ac3efe0f", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "2a2e9257e4d76b6a0303547c69bea48b", "file_size": 1017688, "href": "/files-processed/4DNFIE36RMQE/@@download/4DNFIE36RMQE.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "a425a0f8bb8842a7c8304580f0b30c3d", "file_size": 4323554, "href": "/files-processed/4DNFIE36RMQE/@@download/4DNFIE36RMQE.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:47.913395+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P9 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P09", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P9 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P9 of 16 fractions", "value": "P9 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:59.461463+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P3 - 4DNEXZH8PQ2D", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "78141041-97c6-4a8c-8d88-1545090b283e", "accession": "4DNEXZH8PQ2D", "files": [{"uuid": "1015b316-c9b6-4feb-83f6-07219b10115d", "accession": "4DNFI5K14SNA", "file_classification": "raw file", "display_title": "4DNFI5K14SNA.fastq.gz", "file_size": 1481097967, "href": "/files-fastq/4DNFI5K14SNA/@@download/4DNFI5K14SNA.fastq.gz", "md5sum": "6db4e6daa9313479cc5874a237307c7a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1015b316-c9b6-4feb-83f6-07219b10115d/4DNFI5K14SNA.fastq.gz", "@id": "/files-fastq/4DNFI5K14SNA/", "upload_key": "1015b316-c9b6-4feb-83f6-07219b10115d/4DNFI5K14SNA.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5K14SNA/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 28606485, "uuid": "319055cf-289d-4e05-b30b-e764f447b6cc", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/319055cf-289d-4e05-b30b-e764f447b6cc/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P3 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P03", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXZH8PQ2D/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI6WY9AR7.bam", "upload_key": "6ebbf60d-35bf-45fc-af29-e53625add54b/4DNFI6WY9AR7.bam", "href": "/files-processed/4DNFI6WY9AR7/@@download/4DNFI6WY9AR7.bam", "accession": "4DNFI6WY9AR7", "md5sum": "44fcb0898db38cad41a65344b1fcf14d", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI6WY9AR7/", "file_size": 1307358473, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6ebbf60d-35bf-45fc-af29-e53625add54b/4DNFI6WY9AR7.bam", "file_type_detailed": "alignments (bam)", "uuid": "6ebbf60d-35bf-45fc-af29-e53625add54b", "status": "released", "quality_metric": {"status": "released", "uuid": "32555705-db59-4c96-a620-060b0eef1138", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/32555705-db59-4c96-a620-060b0eef1138/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "23181010", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.558", "tooltip": "Percent of total aligned reads (=0.82m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:45:20.129123+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P3 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P03", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI53HWCWY.bedGraph.gz", "upload_key": "c0a391f2-1127-427d-92c8-fe7ce062a568/4DNFI53HWCWY.bedGraph.gz", "href": "/files-processed/4DNFI53HWCWY/@@download/4DNFI53HWCWY.bedGraph.gz", "accession": "4DNFI53HWCWY", "md5sum": "e48e52d624a9ceed97f2e75325e1c1fb", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'XSZUvxI9RmGSyoRsbgvdUQ'", "@id": "/files-processed/4DNFI53HWCWY/", "file_size": 3913954, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c0a391f2-1127-427d-92c8-fe7ce062a568/4DNFI53HWCWY.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "c0a391f2-1127-427d-92c8-fe7ce062a568", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI53HWCWY - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P3 of 16 fractions", "@id": "/higlass-view-configs/b78f2365-fd89-42de-9aaf-8cf7b28ec3f9/", "uuid": "b78f2365-fd89-42de-9aaf-8cf7b28ec3f9", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "7454a3c831f031b310635547aa1a03be", "file_size": 1018759, "href": "/files-processed/4DNFI53HWCWY/@@download/4DNFI53HWCWY.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "098b1a046ec7213b39d464324d031623", "file_size": 4455276, "href": "/files-processed/4DNFI53HWCWY/@@download/4DNFI53HWCWY.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:55.724374+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P3 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P03", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P3 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P3 of 16 fractions", "value": "P3 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:52.765798+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P16 - 4DNEXYX58PCM", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "a69af64f-6eff-4aee-848f-5e30a51fd533", "accession": "4DNEXYX58PCM", "files": [{"uuid": "80006082-f8a5-4bf7-a402-26029fb8b439", "accession": "4DNFICP5RMMC", "file_classification": "raw file", "display_title": "4DNFICP5RMMC.fastq.gz", "file_size": 1174338508, "href": "/files-fastq/4DNFICP5RMMC/@@download/4DNFICP5RMMC.fastq.gz", "md5sum": "740a3500f84a031c58c6b0ddd193127d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/80006082-f8a5-4bf7-a402-26029fb8b439/4DNFICP5RMMC.fastq.gz", "@id": "/files-fastq/4DNFICP5RMMC/", "upload_key": "80006082-f8a5-4bf7-a402-26029fb8b439/4DNFICP5RMMC.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICP5RMMC/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 24267456, "uuid": "582d4a58-db06-4ffb-bd1d-83475916da49", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/582d4a58-db06-4ffb-bd1d-83475916da49/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P16 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P16", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXYX58PCM/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIZKC814T.bam", "upload_key": "a06bf841-aa69-4094-99c9-6a89a7d70eae/4DNFIZKC814T.bam", "href": "/files-processed/4DNFIZKC814T/@@download/4DNFIZKC814T.bam", "accession": "4DNFIZKC814T", "md5sum": "f3e0b9b9f074c8bd931921e913bc1242", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIZKC814T/", "file_size": 779714984, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a06bf841-aa69-4094-99c9-6a89a7d70eae/4DNFIZKC814T.bam", "file_type_detailed": "alignments (bam)", "uuid": "a06bf841-aa69-4094-99c9-6a89a7d70eae", "status": "released", "quality_metric": {"status": "released", "uuid": "03a7bf73-f267-4eb4-aa00-e3662b3fa6ed", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/03a7bf73-f267-4eb4-aa00-e3662b3fa6ed/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "15626026", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "10.445", "tooltip": "Percent of total aligned reads (=1.63m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:46:50.081040+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P16 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P16", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIUOOXQUY.bedGraph.gz", "upload_key": "a5425f56-9f4d-4e07-ac63-429f622d0234/4DNFIUOOXQUY.bedGraph.gz", "href": "/files-processed/4DNFIUOOXQUY/@@download/4DNFIUOOXQUY.bedGraph.gz", "accession": "4DNFIUOOXQUY", "md5sum": "0f5f94de576f53aa461821104e424a70", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "OooC5zxUQPSu5TFWlCzREQ", "@id": "/files-processed/4DNFIUOOXQUY/", "file_size": 3735388, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a5425f56-9f4d-4e07-ac63-429f622d0234/4DNFIUOOXQUY.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "a5425f56-9f4d-4e07-ac63-429f622d0234", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIUOOXQUY - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P16 of 16 fractions", "@id": "/higlass-view-configs/094937fe-0860-4d09-9d7c-2ced8638fd99/", "uuid": "094937fe-0860-4d09-9d7c-2ced8638fd99", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"href": "/files-processed/4DNFIUOOXQUY/@@download/4DNFIUOOXQUY.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "7da15cce78a5c06d190b95d7a8f5b2ba", "file_size": 4305661, "href": "/files-processed/4DNFIUOOXQUY/@@download/4DNFIUOOXQUY.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:55.256646+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P16 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P16", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P16 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P16 of 16 fractions", "value": "P16 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:11.387439+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P2 - 4DNEXL6WTINA", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "a408f136-aac7-4be7-a332-a2e2032bc25f", "accession": "4DNEXL6WTINA", "files": [{"uuid": "399c63e8-d86a-4350-a7ac-73bd4aefcfd5", "accession": "4DNFID4LYNLR", "file_classification": "raw file", "display_title": "4DNFID4LYNLR.fastq.gz", "file_size": 1283150483, "href": "/files-fastq/4DNFID4LYNLR/@@download/4DNFID4LYNLR.fastq.gz", "md5sum": "459a0f9367609222981d10b067996fe9", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/399c63e8-d86a-4350-a7ac-73bd4aefcfd5/4DNFID4LYNLR.fastq.gz", "@id": "/files-fastq/4DNFID4LYNLR/", "upload_key": "399c63e8-d86a-4350-a7ac-73bd4aefcfd5/4DNFID4LYNLR.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID4LYNLR/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 26394770, "uuid": "545c9afe-ce40-4c40-b47d-b195b689db83", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/545c9afe-ce40-4c40-b47d-b195b689db83/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P2 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P02", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXL6WTINA/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFISZGVUWC.bam", "upload_key": "303eed10-2d9f-40e4-8630-57e84275dafb/4DNFISZGVUWC.bam", "href": "/files-processed/4DNFISZGVUWC/@@download/4DNFISZGVUWC.bam", "accession": "4DNFISZGVUWC", "md5sum": "fc44b748881288dba7745daf5a9951a5", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISZGVUWC/", "file_size": 1042852218, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/303eed10-2d9f-40e4-8630-57e84275dafb/4DNFISZGVUWC.bam", "file_type_detailed": "alignments (bam)", "uuid": "303eed10-2d9f-40e4-8630-57e84275dafb", "status": "released", "quality_metric": {"status": "released", "uuid": "1eb13bf8-2769-4631-8922-f1dfd327400e", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/1eb13bf8-2769-4631-8922-f1dfd327400e/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "21041070", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "10.007", "tooltip": "Percent of total aligned reads (=2.11m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:46:07.184231+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P2 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P02", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI2HVNXQF.bedGraph.gz", "upload_key": "f998ae05-64c0-40b3-a85e-67f407f13e12/4DNFI2HVNXQF.bedGraph.gz", "href": "/files-processed/4DNFI2HVNXQF/@@download/4DNFI2HVNXQF.bedGraph.gz", "accession": "4DNFI2HVNXQF", "md5sum": "b967392b48bf672e3240e8f985f07ca4", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "Lo5L7PEHSLm6kgB7hZQ9-g", "@id": "/files-processed/4DNFI2HVNXQF/", "file_size": 3875119, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f998ae05-64c0-40b3-a85e-67f407f13e12/4DNFI2HVNXQF.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "f998ae05-64c0-40b3-a85e-67f407f13e12", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI2HVNXQF - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P2 of 16 fractions", "@id": "/higlass-view-configs/20294516-3f9f-401f-911f-3a849a711b93/", "uuid": "20294516-3f9f-401f-911f-3a849a711b93", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "01db938b7e6ad5b68b2c1f7a5017d840", "file_size": 1016988, "href": "/files-processed/4DNFI2HVNXQF/@@download/4DNFI2HVNXQF.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"href": "/files-processed/4DNFI2HVNXQF/@@download/4DNFI2HVNXQF.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:36.124933+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P2 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P02", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P2 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P2 of 16 fractions", "value": "P2 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:26.694709+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) G1-phase G1 - 4DNEX6Q73J7B", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "1a176105-b489-494f-a044-668f13fb24f8", "accession": "4DNEX6Q73J7B", "files": [{"uuid": "cef351cd-a732-4ae8-a498-fce6a68e6579", "accession": "4DNFI2PQX3ST", "file_classification": "raw file", "display_title": "4DNFI2PQX3ST.fastq.gz", "file_size": 1265106239, "href": "/files-fastq/4DNFI2PQX3ST/@@download/4DNFI2PQX3ST.fastq.gz", "md5sum": "3c0fb01a2d80e3f516ff3fa1892d7148", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/cef351cd-a732-4ae8-a498-fce6a68e6579/4DNFI2PQX3ST.fastq.gz", "@id": "/files-fastq/4DNFI2PQX3ST/", "upload_key": "cef351cd-a732-4ae8-a498-fce6a68e6579/4DNFI2PQX3ST.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI2PQX3ST/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 26291785, "uuid": "4c265916-cf81-4e4a-a6f2-ebbfb21f9385", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/4c265916-cf81-4e4a-a6f2-ebbfb21f9385/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "G1 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P1-G1 baseline", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX6Q73J7B/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI7F1NCY4.bam", "upload_key": "a43039f1-88ba-4f66-ba33-ceb36e34aff2/4DNFI7F1NCY4.bam", "href": "/files-processed/4DNFI7F1NCY4/@@download/4DNFI7F1NCY4.bam", "accession": "4DNFI7F1NCY4", "md5sum": "f9ca0951ccc10955ebb245f9c920d6f3", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI7F1NCY4/", "file_size": 1076426328, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a43039f1-88ba-4f66-ba33-ceb36e34aff2/4DNFI7F1NCY4.bam", "file_type_detailed": "alignments (bam)", "uuid": "a43039f1-88ba-4f66-ba33-ceb36e34aff2", "status": "released", "quality_metric": {"status": "released", "uuid": "1ca742a6-76c2-4816-b1e9-21417797a2d3", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/1ca742a6-76c2-4816-b1e9-21417797a2d3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "19238901", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "1.034", "tooltip": "Percent of total aligned reads (=0.2m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:41:26.759312+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "G1 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P1-G1 baseline", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIMQCMD7J.bedGraph.gz", "upload_key": "eedd62e0-9bfc-4ac7-9bc1-141d1f318a8c/4DNFIMQCMD7J.bedGraph.gz", "href": "/files-processed/4DNFIMQCMD7J/@@download/4DNFIMQCMD7J.bedGraph.gz", "accession": "4DNFIMQCMD7J", "md5sum": "82160d0ab2f318f8e822c5cae8b46d3b", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'SJOJwIqJQ56W6mYJBI-mkg'", "@id": "/files-processed/4DNFIMQCMD7J/", "file_size": 3788747, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/eedd62e0-9bfc-4ac7-9bc1-141d1f318a8c/4DNFIMQCMD7J.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "eedd62e0-9bfc-4ac7-9bc1-141d1f318a8c", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIMQCMD7J - counts for H1-hESC (Tier 1) Multi-stage Repli-seq G1 of 16 fractions", "@id": "/higlass-view-configs/aaa4e889-9d66-45c3-b0b0-9f83aa81ec1f/", "uuid": "aaa4e889-9d66-45c3-b0b0-9f83aa81ec1f", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "67b7901a7748a3b0037e94d60d905225", "file_size": 1017007, "href": "/files-processed/4DNFIMQCMD7J/@@download/4DNFIMQCMD7J.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "55606aa18bad13a8eddaf311bb2140d6", "file_size": 4377767, "href": "/files-processed/4DNFIMQCMD7J/@@download/4DNFIMQCMD7J.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:58.359207+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "G1 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P1-G1 baseline", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq G1 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: G1 of 16 fractions", "value": "G1 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:50.586929+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P4 - 4DNEX7KPBKXE", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "de1d01c6-2397-4935-936b-71917ca4649b", "accession": "4DNEX7KPBKXE", "files": [{"uuid": "417db7b4-1e5d-4ae0-a8a5-c28b9294a81d", "accession": "4DNFI7MNY99T", "file_classification": "raw file", "display_title": "4DNFI7MNY99T.fastq.gz", "file_size": 1627077454, "href": "/files-fastq/4DNFI7MNY99T/@@download/4DNFI7MNY99T.fastq.gz", "md5sum": "9f4aa873d6461245aa47f26d96b7fac6", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/417db7b4-1e5d-4ae0-a8a5-c28b9294a81d/4DNFI7MNY99T.fastq.gz", "@id": "/files-fastq/4DNFI7MNY99T/", "upload_key": "417db7b4-1e5d-4ae0-a8a5-c28b9294a81d/4DNFI7MNY99T.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7MNY99T/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33558826, "uuid": "576911dd-6abe-470a-bc39-6dc16273e832", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/576911dd-6abe-470a-bc39-6dc16273e832/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P4 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P04", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX7KPBKXE/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI44MKR9P.bam", "upload_key": "b84b7844-d864-4ee5-b839-adb7162e81bb/4DNFI44MKR9P.bam", "href": "/files-processed/4DNFI44MKR9P/@@download/4DNFI44MKR9P.bam", "accession": "4DNFI44MKR9P", "md5sum": "6d54c67e91148a3c826fd1f1c39ce673", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI44MKR9P/", "file_size": 1402390257, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b84b7844-d864-4ee5-b839-adb7162e81bb/4DNFI44MKR9P.bam", "file_type_detailed": "alignments (bam)", "uuid": "b84b7844-d864-4ee5-b839-adb7162e81bb", "status": "released", "quality_metric": {"status": "released", "uuid": "10709769-7549-4139-a01b-1511d0503d01", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/10709769-7549-4139-a01b-1511d0503d01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "27142050", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "5.459", "tooltip": "Percent of total aligned reads (=1.48m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:57.517599+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P4 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P04", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI9WSOV8G.bedGraph.gz", "upload_key": "fd5c6abd-b7bb-437d-aacd-adc31135823d/4DNFI9WSOV8G.bedGraph.gz", "href": "/files-processed/4DNFI9WSOV8G/@@download/4DNFI9WSOV8G.bedGraph.gz", "accession": "4DNFI9WSOV8G", "md5sum": "831347ea71bdc9c08567b7600d6fb0be", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'BYroofmdSwu3aluTqt4n-w'", "@id": "/files-processed/4DNFI9WSOV8G/", "file_size": 3933104, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fd5c6abd-b7bb-437d-aacd-adc31135823d/4DNFI9WSOV8G.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "fd5c6abd-b7bb-437d-aacd-adc31135823d", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI9WSOV8G - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P4 of 16 fractions", "@id": "/higlass-view-configs/ba0892ed-396e-4e30-8170-07c3076406eb/", "uuid": "ba0892ed-396e-4e30-8170-07c3076406eb", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "00809b338ebdf5ef3fefbe5b52655483", "file_size": 1018041, "href": "/files-processed/4DNFI9WSOV8G/@@download/4DNFI9WSOV8G.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "9e10c13fdca70c58043143bebf329659", "file_size": 4482077, "href": "/files-processed/4DNFI9WSOV8G/@@download/4DNFI9WSOV8G.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:54.300927+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P4 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P04", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P4 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P4 of 16 fractions", "value": "P4 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:53.907684+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P12 - 4DNEX1BWBWFA", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "b2c67621-de42-4301-bf47-386f5d79f326", "accession": "4DNEX1BWBWFA", "files": [{"uuid": "4ed4907b-7a46-4e72-b9ac-696ee8da0570", "accession": "4DNFIKDI9FT6", "file_classification": "raw file", "display_title": "4DNFIKDI9FT6.fastq.gz", "file_size": 1609535989, "href": "/files-fastq/4DNFIKDI9FT6/@@download/4DNFIKDI9FT6.fastq.gz", "md5sum": "204ec623492406f4b832248f9d03b0bb", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4ed4907b-7a46-4e72-b9ac-696ee8da0570/4DNFIKDI9FT6.fastq.gz", "@id": "/files-fastq/4DNFIKDI9FT6/", "upload_key": "4ed4907b-7a46-4e72-b9ac-696ee8da0570/4DNFIKDI9FT6.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKDI9FT6/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33202243, "uuid": "79b8b290-ce39-4437-b51f-774acaa00640", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/79b8b290-ce39-4437-b51f-774acaa00640/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P12 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P12", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX1BWBWFA/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFISTD47QS.bam", "upload_key": "f16926c1-43b1-486d-86c0-dbc03ad206f2/4DNFISTD47QS.bam", "href": "/files-processed/4DNFISTD47QS/@@download/4DNFISTD47QS.bam", "accession": "4DNFISTD47QS", "md5sum": "ba58425a24dfb9502ffe03ef275caceb", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISTD47QS/", "file_size": 1456808754, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f16926c1-43b1-486d-86c0-dbc03ad206f2/4DNFISTD47QS.bam", "file_type_detailed": "alignments (bam)", "uuid": "f16926c1-43b1-486d-86c0-dbc03ad206f2", "status": "released", "quality_metric": {"status": "released", "uuid": "7308d3a4-00cb-4513-b8ed-942bdd904dea", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/7308d3a4-00cb-4513-b8ed-942bdd904dea/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "27473902", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.827", "tooltip": "Percent of total aligned reads (=1.05m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:43.683118+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P12 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P12", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIMT1AIDU.bedGraph.gz", "upload_key": "2db087cc-5170-47aa-9a5e-cd4cfc9a341f/4DNFIMT1AIDU.bedGraph.gz", "href": "/files-processed/4DNFIMT1AIDU/@@download/4DNFIMT1AIDU.bedGraph.gz", "accession": "4DNFIMT1AIDU", "md5sum": "df6d5f43e5f60bc5e3eab29b91c68455", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "AAOax3jYR1CqjIbYmyimRg", "@id": "/files-processed/4DNFIMT1AIDU/", "file_size": 3967211, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2db087cc-5170-47aa-9a5e-cd4cfc9a341f/4DNFIMT1AIDU.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "2db087cc-5170-47aa-9a5e-cd4cfc9a341f", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIMT1AIDU - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P12 of 16 fractions", "@id": "/higlass-view-configs/d0dd5af8-8c65-4f83-b69a-e216d08b8f7b/", "uuid": "d0dd5af8-8c65-4f83-b69a-e216d08b8f7b", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "79ebe8fd24239e9caa0b3a7a43abbcdc", "file_size": 1018627, "href": "/files-processed/4DNFIMT1AIDU/@@download/4DNFIMT1AIDU.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "28579c75c8aebe999ae185957fc2997c", "file_size": 4480635, "href": "/files-processed/4DNFIMT1AIDU/@@download/4DNFIMT1AIDU.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:49.619085+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P12 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P12", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P12 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P12 of 16 fractions", "value": "P12 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:16.172757+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) G1-phase G1 - 4DNEXDRZLEQV", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "2a241f5c-f2f2-44ce-a0dd-264e38be62f0", "accession": "4DNEXDRZLEQV", "files": [{"uuid": "b96526eb-b6c7-4a25-98f1-e74e046ac551", "accession": "4DNFIO5IUBAD", "file_classification": "raw file", "display_title": "4DNFIO5IUBAD.fastq.gz", "file_size": 1165472835, "href": "/files-fastq/4DNFIO5IUBAD/@@download/4DNFIO5IUBAD.fastq.gz", "md5sum": "1026ed672037ea972401493394171e2b", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b96526eb-b6c7-4a25-98f1-e74e046ac551/4DNFIO5IUBAD.fastq.gz", "@id": "/files-fastq/4DNFIO5IUBAD/", "upload_key": "b96526eb-b6c7-4a25-98f1-e74e046ac551/4DNFIO5IUBAD.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIO5IUBAD/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 24126671, "uuid": "2f14881f-2fbb-4da0-838c-e079e9ce33a3", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/2f14881f-2fbb-4da0-838c-e079e9ce33a3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "G1 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P1-G1 baseline", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXDRZLEQV/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIICI1L91.bam", "upload_key": "c7b8a6de-b577-4837-98c6-e4d96bf1cf7f/4DNFIICI1L91.bam", "href": "/files-processed/4DNFIICI1L91/@@download/4DNFIICI1L91.bam", "accession": "4DNFIICI1L91", "md5sum": "24a98b36e784769e499086085a76babd", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIICI1L91/", "file_size": 1065406400, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c7b8a6de-b577-4837-98c6-e4d96bf1cf7f/4DNFIICI1L91.bam", "file_type_detailed": "alignments (bam)", "uuid": "c7b8a6de-b577-4837-98c6-e4d96bf1cf7f", "status": "released", "quality_metric": {"status": "released", "uuid": "2dbcff0e-3f65-4db2-839f-7fa9f7875525", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/2dbcff0e-3f65-4db2-839f-7fa9f7875525/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "19378813", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "1.924", "tooltip": "Percent of total aligned reads (=0.37m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:32.375925+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "G1 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P1-G1 baseline", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI55KQMBA.bedGraph.gz", "upload_key": "66ae4d73-d8ae-4d36-89ee-4b5dae345e2f/4DNFI55KQMBA.bedGraph.gz", "href": "/files-processed/4DNFI55KQMBA/@@download/4DNFI55KQMBA.bedGraph.gz", "accession": "4DNFI55KQMBA", "md5sum": "bce2a3d94e42d628884fcca2afdb818b", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "WpHQvzPhRfSqMm1ZvDThmw", "@id": "/files-processed/4DNFI55KQMBA/", "file_size": 3724935, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/66ae4d73-d8ae-4d36-89ee-4b5dae345e2f/4DNFI55KQMBA.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "66ae4d73-d8ae-4d36-89ee-4b5dae345e2f", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI55KQMBA - counts for H1-hESC (Tier 1) Multi-stage Repli-seq G1 of 16 fractions", "@id": "/higlass-view-configs/5656afec-76da-4745-b9dd-50a385f0ea98/", "uuid": "5656afec-76da-4745-b9dd-50a385f0ea98", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "5f2f211a3c95271367af7ef66c84eed1", "file_size": 1016635, "href": "/files-processed/4DNFI55KQMBA/@@download/4DNFI55KQMBA.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "5a5056c58eea073ca68ca4dffadac254", "file_size": 4329539, "href": "/files-processed/4DNFI55KQMBA/@@download/4DNFI55KQMBA.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:34.974284+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "G1 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P1-G1 baseline", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq G1 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: G1 of 16 fractions", "value": "G1 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:28.099681+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P14 - 4DNEXFRYPDNV", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "4e365c80-db36-4279-8c31-ec088ebdafa2", "accession": "4DNEXFRYPDNV", "files": [{"uuid": "0c121598-3aae-4e93-9714-05139f038ae5", "accession": "4DNFID4HG1GR", "file_classification": "raw file", "display_title": "4DNFID4HG1GR.fastq.gz", "file_size": 1554833942, "href": "/files-fastq/4DNFID4HG1GR/@@download/4DNFID4HG1GR.fastq.gz", "md5sum": "5b478c0c33a99123d77f83c4cdf5ada3", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0c121598-3aae-4e93-9714-05139f038ae5/4DNFID4HG1GR.fastq.gz", "@id": "/files-fastq/4DNFID4HG1GR/", "upload_key": "0c121598-3aae-4e93-9714-05139f038ae5/4DNFID4HG1GR.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID4HG1GR/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 32357002, "uuid": "c8554a46-434c-4014-87c3-964d2ffd61a2", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/c8554a46-434c-4014-87c3-964d2ffd61a2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P14 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P14", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXFRYPDNV/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIU5KPNL9.bam", "upload_key": "e26d19bc-b933-43be-9165-405b5ff7a370/4DNFIU5KPNL9.bam", "href": "/files-processed/4DNFIU5KPNL9/@@download/4DNFIU5KPNL9.bam", "accession": "4DNFIU5KPNL9", "md5sum": "1a45ad05e601528b903fec901de80b09", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIU5KPNL9/", "file_size": 1285885088, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e26d19bc-b933-43be-9165-405b5ff7a370/4DNFIU5KPNL9.bam", "file_type_detailed": "alignments (bam)", "uuid": "e26d19bc-b933-43be-9165-405b5ff7a370", "status": "released", "quality_metric": {"status": "released", "uuid": "26fa662f-6256-4904-832f-f25b887ae5cb", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/26fa662f-6256-4904-832f-f25b887ae5cb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "24383737", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.745", "tooltip": "Percent of total aligned reads (=1.16m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:43.975663+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P14 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P14", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIQMOXIPL.bedGraph.gz", "upload_key": "f2c96bd5-9645-4b52-85ec-f37586749612/4DNFIQMOXIPL.bedGraph.gz", "href": "/files-processed/4DNFIQMOXIPL/@@download/4DNFIQMOXIPL.bedGraph.gz", "accession": "4DNFIQMOXIPL", "md5sum": "a2a63882d174264e75960a41b644ff21", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'WerT5jxNQsC-bC9KyXXcRA'", "@id": "/files-processed/4DNFIQMOXIPL/", "file_size": 3890151, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f2c96bd5-9645-4b52-85ec-f37586749612/4DNFIQMOXIPL.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "f2c96bd5-9645-4b52-85ec-f37586749612", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIQMOXIPL - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P14 of 16 fractions", "@id": "/higlass-view-configs/07407e41-291c-44ef-8b63-29fadab6afe7/", "uuid": "07407e41-291c-44ef-8b63-29fadab6afe7", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "ea8974aa6c8b9119b583b2939b95f96c", "file_size": 1017775, "href": "/files-processed/4DNFIQMOXIPL/@@download/4DNFIQMOXIPL.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "0d0d24dc124a4b40bde7ae888045f52a", "file_size": 4437530, "href": "/files-processed/4DNFIQMOXIPL/@@download/4DNFIQMOXIPL.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:40.955093+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P14 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P14", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P14 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P14 of 16 fractions", "value": "P14 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:05.710002+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P15 - 4DNEXCTB91SG", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "a06f8505-a520-4bfe-bac8-72c9d786b47f", "accession": "4DNEXCTB91SG", "files": [{"uuid": "7923ad2d-f200-4dc3-ae4a-5609da48d116", "accession": "4DNFI11PGFD3", "file_classification": "raw file", "display_title": "4DNFI11PGFD3.fastq.gz", "file_size": 1030227352, "href": "/files-fastq/4DNFI11PGFD3/@@download/4DNFI11PGFD3.fastq.gz", "md5sum": "4439314d7c641a16baaf99dd4a80e69f", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/7923ad2d-f200-4dc3-ae4a-5609da48d116/4DNFI11PGFD3.fastq.gz", "@id": "/files-fastq/4DNFI11PGFD3/", "upload_key": "7923ad2d-f200-4dc3-ae4a-5609da48d116/4DNFI11PGFD3.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI11PGFD3/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 21378193, "uuid": "998be7bf-7b80-4de0-8afe-b55dc17ffebd", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/998be7bf-7b80-4de0-8afe-b55dc17ffebd/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P15 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P15", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXCTB91SG/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIHNZT64Y.bam", "upload_key": "c8129e35-cd0f-4c2b-8d84-a48300a3b65d/4DNFIHNZT64Y.bam", "href": "/files-processed/4DNFIHNZT64Y/@@download/4DNFIHNZT64Y.bam", "accession": "4DNFIHNZT64Y", "md5sum": "b8242e96fcb070811d0431ea3f5440c1", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIHNZT64Y/", "file_size": 550560806, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c8129e35-cd0f-4c2b-8d84-a48300a3b65d/4DNFIHNZT64Y.bam", "file_type_detailed": "alignments (bam)", "uuid": "c8129e35-cd0f-4c2b-8d84-a48300a3b65d", "status": "released", "quality_metric": {"status": "released", "uuid": "162be49c-990e-4031-93c8-fc090e9815f2", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/162be49c-990e-4031-93c8-fc090e9815f2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "14696241", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "31.034", "tooltip": "Percent of total aligned reads (=4.56m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:18.715382+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P15 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P15", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIB7HIKV7.bedGraph.gz", "upload_key": "0982285b-1742-4256-b47c-020413f58627/4DNFIB7HIKV7.bedGraph.gz", "href": "/files-processed/4DNFIB7HIKV7/@@download/4DNFIB7HIKV7.bedGraph.gz", "accession": "4DNFIB7HIKV7", "md5sum": "59bbbd0d21b77ba9a175bb0490002d97", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "CrESqTHRSSCkXXTI-sIVdg", "@id": "/files-processed/4DNFIB7HIKV7/", "file_size": 3647720, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0982285b-1742-4256-b47c-020413f58627/4DNFIB7HIKV7.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "0982285b-1742-4256-b47c-020413f58627", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIB7HIKV7 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P15 of 16 fractions", "@id": "/higlass-view-configs/261da1d5-307b-48b3-99de-ab105f3fbfcf/", "uuid": "261da1d5-307b-48b3-99de-ab105f3fbfcf", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "89fefe817e0e672fdbcee6a565d88b0b", "file_size": 1016888, "href": "/files-processed/4DNFIB7HIKV7/@@download/4DNFIB7HIKV7.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "a870b28fd9b5cac464de6f8800314649", "file_size": 4220787, "href": "/files-processed/4DNFIB7HIKV7/@@download/4DNFIB7HIKV7.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:53.853880+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P15 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P15", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P15 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P15 of 16 fractions", "value": "P15 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:12.522232+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P6 - 4DNEXJ9B1OWZ", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "40fb1b98-9a14-41e4-bca8-9e3d1321b28f", "accession": "4DNEXJ9B1OWZ", "files": [{"uuid": "a553613b-3402-4f00-af74-2df8c0ca1a14", "accession": "4DNFI3Z6V8QQ", "file_classification": "raw file", "display_title": "4DNFI3Z6V8QQ.fastq.gz", "file_size": 1737005231, "href": "/files-fastq/4DNFI3Z6V8QQ/@@download/4DNFI3Z6V8QQ.fastq.gz", "md5sum": "7e9b79ba5797f9ec9ae8c3fab65508bc", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a553613b-3402-4f00-af74-2df8c0ca1a14/4DNFI3Z6V8QQ.fastq.gz", "@id": "/files-fastq/4DNFI3Z6V8QQ/", "upload_key": "a553613b-3402-4f00-af74-2df8c0ca1a14/4DNFI3Z6V8QQ.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3Z6V8QQ/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 35644481, "uuid": "f3a9c72a-eb8e-4ef4-a451-0922ac093757", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/f3a9c72a-eb8e-4ef4-a451-0922ac093757/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P6 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P06", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXJ9B1OWZ/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIUWITQRT.bam", "upload_key": "fbef57b6-b5e3-4f1d-8abd-f0764937977b/4DNFIUWITQRT.bam", "href": "/files-processed/4DNFIUWITQRT/@@download/4DNFIUWITQRT.bam", "accession": "4DNFIUWITQRT", "md5sum": "35b3e16d5f49700132052b59eeeaecf0", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIUWITQRT/", "file_size": 1553320018, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fbef57b6-b5e3-4f1d-8abd-f0764937977b/4DNFIUWITQRT.bam", "file_type_detailed": "alignments (bam)", "uuid": "fbef57b6-b5e3-4f1d-8abd-f0764937977b", "status": "released", "quality_metric": {"status": "released", "uuid": "b03140b8-bf06-44e8-90ea-6bede504a975", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/b03140b8-bf06-44e8-90ea-6bede504a975/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "29367540", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.309", "tooltip": "Percent of total aligned reads (=1.27m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:49.435346+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P6 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P06", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIF123DPU.bedGraph.gz", "upload_key": "b2280f49-e9e7-43eb-ae27-45c69e42df99/4DNFIF123DPU.bedGraph.gz", "href": "/files-processed/4DNFIF123DPU/@@download/4DNFIF123DPU.bedGraph.gz", "accession": "4DNFIF123DPU", "md5sum": "d6a3150d2777be82c3534dce77f7af22", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'AXmNNYMfSaSItJqwW29oYA'", "@id": "/files-processed/4DNFIF123DPU/", "file_size": 3988954, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b2280f49-e9e7-43eb-ae27-45c69e42df99/4DNFIF123DPU.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "b2280f49-e9e7-43eb-ae27-45c69e42df99", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIF123DPU - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P6 of 16 fractions", "@id": "/higlass-view-configs/36f2e84e-baef-40f8-abda-40adc2f2ebf4/", "uuid": "36f2e84e-baef-40f8-abda-40adc2f2ebf4", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "f227165aaed3720af01293efc855e2de", "file_size": 1018118, "href": "/files-processed/4DNFIF123DPU/@@download/4DNFIF123DPU.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "16d390fb7b3d5b628a2bca39f330b168", "file_size": 4500188, "href": "/files-processed/4DNFIF123DPU/@@download/4DNFIF123DPU.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:51.696595+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P6 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P06", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P6 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P6 of 16 fractions", "value": "P6 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:56.098650+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P15 - 4DNEX65GM2L2", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "0f3f8eec-2cb9-4ba8-8dfd-16a9dfbaec71", "accession": "4DNEX65GM2L2", "files": [{"uuid": "998457e8-e578-4062-8b57-f4e491754464", "accession": "4DNFISL55MDZ", "file_classification": "raw file", "display_title": "4DNFISL55MDZ.fastq.gz", "file_size": 1333419097, "href": "/files-fastq/4DNFISL55MDZ/@@download/4DNFISL55MDZ.fastq.gz", "md5sum": "96cf630fd209860448468311145a2a7c", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/998457e8-e578-4062-8b57-f4e491754464/4DNFISL55MDZ.fastq.gz", "@id": "/files-fastq/4DNFISL55MDZ/", "upload_key": "998457e8-e578-4062-8b57-f4e491754464/4DNFISL55MDZ.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFISL55MDZ/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 25920150, "uuid": "ab16e7fa-8d2f-46be-8922-7c609b9ac54d", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/ab16e7fa-8d2f-46be-8922-7c609b9ac54d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P15 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P15", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX65GM2L2/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI84EUQI8.bam", "upload_key": "8b3abc53-ae8b-451c-9a8c-d974b5e4903a/4DNFI84EUQI8.bam", "href": "/files-processed/4DNFI84EUQI8/@@download/4DNFI84EUQI8.bam", "accession": "4DNFI84EUQI8", "md5sum": "faf73f32617ba1c30e070e02d8493127", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI84EUQI8/", "file_size": 1084497416, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8b3abc53-ae8b-451c-9a8c-d974b5e4903a/4DNFI84EUQI8.bam", "file_type_detailed": "alignments (bam)", "uuid": "8b3abc53-ae8b-451c-9a8c-d974b5e4903a", "status": "released", "quality_metric": {"status": "released", "uuid": "63c9f980-28a6-400e-92fd-fdf94df30698", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/63c9f980-28a6-400e-92fd-fdf94df30698/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "19055047", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.547", "tooltip": "Percent of total aligned reads (=0.87m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:05.171490+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P15 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P15", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIF74VPT2.bedGraph.gz", "upload_key": "a76dbb5e-b01b-47cf-ba81-6324f63350c7/4DNFIF74VPT2.bedGraph.gz", "href": "/files-processed/4DNFIF74VPT2/@@download/4DNFIF74VPT2.bedGraph.gz", "accession": "4DNFIF74VPT2", "md5sum": "ff6da03c5fec407a6cd8486616a8afb9", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'Gpn26fVdRV6WFGjsasg8oQ'", "@id": "/files-processed/4DNFIF74VPT2/", "file_size": 3790174, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a76dbb5e-b01b-47cf-ba81-6324f63350c7/4DNFIF74VPT2.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "a76dbb5e-b01b-47cf-ba81-6324f63350c7", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIF74VPT2 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P15 of 16 fractions", "@id": "/higlass-view-configs/392d7461-370d-483e-a3f4-e0ed3490448d/", "uuid": "392d7461-370d-483e-a3f4-e0ed3490448d", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "48bf51825d4ac7d83b8e6c880a5d1241", "file_size": 1017329, "href": "/files-processed/4DNFIF74VPT2/@@download/4DNFIF74VPT2.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "e652a83f7db90a24a7d2c384ff59858f", "file_size": 4368775, "href": "/files-processed/4DNFIF74VPT2/@@download/4DNFIF74VPT2.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:39.467870+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P15 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P15", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P15 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P15 of 16 fractions", "value": "P15 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:06.724504+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P9 - 4DNEXTM3PBS3", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "15862f9f-7328-4bbe-a726-fb0710e4adf8", "accession": "4DNEXTM3PBS3", "files": [{"uuid": "5db7a430-eece-45f8-beb9-9edb0438a269", "accession": "4DNFI5F69AES", "file_classification": "raw file", "display_title": "4DNFI5F69AES.fastq.gz", "file_size": 1739039585, "href": "/files-fastq/4DNFI5F69AES/@@download/4DNFI5F69AES.fastq.gz", "md5sum": "a8b7fabfb33233ca88332f0e68063fe1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5db7a430-eece-45f8-beb9-9edb0438a269/4DNFI5F69AES.fastq.gz", "@id": "/files-fastq/4DNFI5F69AES/", "upload_key": "5db7a430-eece-45f8-beb9-9edb0438a269/4DNFI5F69AES.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5F69AES/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 35806832, "uuid": "826a7963-7f71-4f25-b9a4-2edec8e78e36", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/826a7963-7f71-4f25-b9a4-2edec8e78e36/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P9 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P09", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXTM3PBS3/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIDL87H1F.bam", "upload_key": "6162dbf7-07af-4b05-87a4-b91d5557f394/4DNFIDL87H1F.bam", "href": "/files-processed/4DNFIDL87H1F/@@download/4DNFIDL87H1F.bam", "accession": "4DNFIDL87H1F", "md5sum": "80d186731414dbeb3a0e78168495d237", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIDL87H1F/", "file_size": 1605356512, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6162dbf7-07af-4b05-87a4-b91d5557f394/4DNFIDL87H1F.bam", "file_type_detailed": "alignments (bam)", "uuid": "6162dbf7-07af-4b05-87a4-b91d5557f394", "status": "released", "quality_metric": {"status": "released", "uuid": "908143cf-07cc-4324-9568-7e8923b37975", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/908143cf-07cc-4324-9568-7e8923b37975/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "30245322", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.551", "tooltip": "Percent of total aligned reads (=1.07m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:26.111682+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P9 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P09", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIOR3SP9L.bedGraph.gz", "upload_key": "573baae1-540c-4f6a-89e0-b273122f8c07/4DNFIOR3SP9L.bedGraph.gz", "href": "/files-processed/4DNFIOR3SP9L/@@download/4DNFIOR3SP9L.bedGraph.gz", "accession": "4DNFIOR3SP9L", "md5sum": "c7d55da09fd93e1947650e2ce5864951", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "Z9O61E-9QpyCp6n0msTZVw", "@id": "/files-processed/4DNFIOR3SP9L/", "file_size": 4031698, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/573baae1-540c-4f6a-89e0-b273122f8c07/4DNFIOR3SP9L.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "573baae1-540c-4f6a-89e0-b273122f8c07", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIOR3SP9L - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P9 of 16 fractions", "@id": "/higlass-view-configs/948c6c15-591a-4393-b6ae-a35b45348cb0/", "uuid": "948c6c15-591a-4393-b6ae-a35b45348cb0", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "355cc23e9fa360bd3962c29f9c1d93e2", "file_size": 1018135, "href": "/files-processed/4DNFIOR3SP9L/@@download/4DNFIOR3SP9L.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "44ae9cf468ab2a83ec7c28a20a7619af", "file_size": 4524120, "href": "/files-processed/4DNFIOR3SP9L/@@download/4DNFIOR3SP9L.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:45.527967+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P9 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P09", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P9 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P9 of 16 fractions", "value": "P9 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:19.228844+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P10 - 4DNEXDWEK1ME", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "40f340df-7f5e-4984-84f7-90e819769007", "accession": "4DNEXDWEK1ME", "files": [{"uuid": "ed13300f-4a0b-4161-b755-526ecadd1b65", "accession": "4DNFIAFVHD6X", "file_classification": "raw file", "display_title": "4DNFIAFVHD6X.fastq.gz", "file_size": 1583020251, "href": "/files-fastq/4DNFIAFVHD6X/@@download/4DNFIAFVHD6X.fastq.gz", "md5sum": "a3161d488de18d43a93a0ef9c88eccce", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ed13300f-4a0b-4161-b755-526ecadd1b65/4DNFIAFVHD6X.fastq.gz", "@id": "/files-fastq/4DNFIAFVHD6X/", "upload_key": "ed13300f-4a0b-4161-b755-526ecadd1b65/4DNFIAFVHD6X.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAFVHD6X/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 32640313, "uuid": "df6513f8-e3cb-49bb-aa73-118d4b0678f5", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/df6513f8-e3cb-49bb-aa73-118d4b0678f5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P10 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P10", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXDWEK1ME/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFILZMYWJV.bam", "upload_key": "977902f6-6d0e-41d0-a2c2-63035fbc33be/4DNFILZMYWJV.bam", "href": "/files-processed/4DNFILZMYWJV/@@download/4DNFILZMYWJV.bam", "accession": "4DNFILZMYWJV", "md5sum": "8be43188cdf5d3eaffa645db0ade05c3", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFILZMYWJV/", "file_size": 1461081658, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/977902f6-6d0e-41d0-a2c2-63035fbc33be/4DNFILZMYWJV.bam", "file_type_detailed": "alignments (bam)", "uuid": "977902f6-6d0e-41d0-a2c2-63035fbc33be", "status": "released", "quality_metric": {"status": "released", "uuid": "6719cb14-4d02-4f34-8210-ab8986b60425", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/6719cb14-4d02-4f34-8210-ab8986b60425/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "27555338", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.996", "tooltip": "Percent of total aligned reads (=1.1m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:46.577010+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P10 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P10", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIN8PMIFN.bedGraph.gz", "upload_key": "e17cc1ec-eb33-4216-9f00-34e8fdc49f75/4DNFIN8PMIFN.bedGraph.gz", "href": "/files-processed/4DNFIN8PMIFN/@@download/4DNFIN8PMIFN.bedGraph.gz", "accession": "4DNFIN8PMIFN", "md5sum": "ee0d9793a5a2fc28b34e4a73a79ce943", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "ZY8nbXqaQbaOfLlIUiPFSw", "@id": "/files-processed/4DNFIN8PMIFN/", "file_size": 3990474, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e17cc1ec-eb33-4216-9f00-34e8fdc49f75/4DNFIN8PMIFN.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "e17cc1ec-eb33-4216-9f00-34e8fdc49f75", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIN8PMIFN - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P10 of 16 fractions", "@id": "/higlass-view-configs/9fce0f4a-5b5b-4b5f-a79a-162c6c7bad4f/", "uuid": "9fce0f4a-5b5b-4b5f-a79a-162c6c7bad4f", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "95f568d9bf0a180b44ad087d070874da", "file_size": 1018590, "href": "/files-processed/4DNFIN8PMIFN/@@download/4DNFIN8PMIFN.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "cc237b82e7ab8d2631f889d67934272b", "file_size": 4494811, "href": "/files-processed/4DNFIN8PMIFN/@@download/4DNFIN8PMIFN.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:46.883171+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P10 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P10", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P10 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P10 of 16 fractions", "value": "P10 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:18.261468+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P7 - 4DNEXS77PTUK", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "d47f0738-e001-493e-b378-4d2ed1d33a4c", "accession": "4DNEXS77PTUK", "files": [{"uuid": "a3449d2b-eb74-4e4b-a132-7f64032df777", "accession": "4DNFI64QYB2B", "file_classification": "raw file", "display_title": "4DNFI64QYB2B.fastq.gz", "file_size": 1629086305, "href": "/files-fastq/4DNFI64QYB2B/@@download/4DNFI64QYB2B.fastq.gz", "md5sum": "4dfba2b874dea57cccb5ffff39ddfbed", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a3449d2b-eb74-4e4b-a132-7f64032df777/4DNFI64QYB2B.fastq.gz", "@id": "/files-fastq/4DNFI64QYB2B/", "upload_key": "a3449d2b-eb74-4e4b-a132-7f64032df777/4DNFI64QYB2B.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI64QYB2B/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33487726, "uuid": "9485ff58-467b-43ec-bd46-df045c3fe2e3", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/9485ff58-467b-43ec-bd46-df045c3fe2e3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P7 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P07", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXS77PTUK/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIM2ZYTN6.bam", "upload_key": "c440abbb-89d6-4e44-af53-dcd0ef3ed83a/4DNFIM2ZYTN6.bam", "href": "/files-processed/4DNFIM2ZYTN6/@@download/4DNFIM2ZYTN6.bam", "accession": "4DNFIM2ZYTN6", "md5sum": "aae97a7e4396a56b3bee53cb930eb9a1", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIM2ZYTN6/", "file_size": 1504786324, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c440abbb-89d6-4e44-af53-dcd0ef3ed83a/4DNFIM2ZYTN6.bam", "file_type_detailed": "alignments (bam)", "uuid": "c440abbb-89d6-4e44-af53-dcd0ef3ed83a", "status": "released", "quality_metric": {"status": "released", "uuid": "22c93ab1-44d9-40ad-9619-f0abf0145585", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/22c93ab1-44d9-40ad-9619-f0abf0145585/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "28326171", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.892", "tooltip": "Percent of total aligned reads (=1.1m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:40.649215+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P7 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P07", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIY1ZLFI6.bedGraph.gz", "upload_key": "1cc142fb-e3ce-44d8-8cef-64ed828e220e/4DNFIY1ZLFI6.bedGraph.gz", "href": "/files-processed/4DNFIY1ZLFI6/@@download/4DNFIY1ZLFI6.bedGraph.gz", "accession": "4DNFIY1ZLFI6", "md5sum": "a91e1c593b55d4c698cd1fc8a4984967", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "Al3xRsQdQROuTafLS6UO0A", "@id": "/files-processed/4DNFIY1ZLFI6/", "file_size": 3992757, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1cc142fb-e3ce-44d8-8cef-64ed828e220e/4DNFIY1ZLFI6.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "1cc142fb-e3ce-44d8-8cef-64ed828e220e", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIY1ZLFI6 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P7 of 16 fractions", "@id": "/higlass-view-configs/a602f4f1-6cfc-41f9-ace6-b340b5bfad1a/", "uuid": "a602f4f1-6cfc-41f9-ace6-b340b5bfad1a", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "e2d4688391d4805cba265a6094987894", "file_size": 1017899, "href": "/files-processed/4DNFIY1ZLFI6/@@download/4DNFIY1ZLFI6.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "87ce50d3c531ff4f92e1861565b54357", "file_size": 4487467, "href": "/files-processed/4DNFIY1ZLFI6/@@download/4DNFIY1ZLFI6.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:42.616600+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P7 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P07", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P7 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P7 of 16 fractions", "value": "P7 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:21.349255+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P13 - 4DNEX5DWF6FC", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "2438645a-5c4f-43ce-9b11-8937b9afa97b", "accession": "4DNEX5DWF6FC", "files": [{"uuid": "f41656a3-d849-427a-9bf4-fb9a20ff002b", "accession": "4DNFIRZBJ7S7", "file_classification": "raw file", "display_title": "4DNFIRZBJ7S7.fastq.gz", "file_size": 1306536857, "href": "/files-fastq/4DNFIRZBJ7S7/@@download/4DNFIRZBJ7S7.fastq.gz", "md5sum": "6a892ee781f15341a2c3099fb64fea51", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f41656a3-d849-427a-9bf4-fb9a20ff002b/4DNFIRZBJ7S7.fastq.gz", "@id": "/files-fastq/4DNFIRZBJ7S7/", "upload_key": "f41656a3-d849-427a-9bf4-fb9a20ff002b/4DNFIRZBJ7S7.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIRZBJ7S7/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 27313956, "uuid": "53a8f97a-d57e-4ba7-ba71-c93a1611ef50", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/53a8f97a-d57e-4ba7-ba71-c93a1611ef50/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P13 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P13", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX5DWF6FC/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIPHD1GA6.bam", "upload_key": "3153e2b3-48bc-4d6b-bee4-aece051c471c/4DNFIPHD1GA6.bam", "href": "/files-processed/4DNFIPHD1GA6/@@download/4DNFIPHD1GA6.bam", "accession": "4DNFIPHD1GA6", "md5sum": "aee85a10ca3d10d182d41e9b009e5c92", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIPHD1GA6/", "file_size": 1159962803, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3153e2b3-48bc-4d6b-bee4-aece051c471c/4DNFIPHD1GA6.bam", "file_type_detailed": "alignments (bam)", "uuid": "3153e2b3-48bc-4d6b-bee4-aece051c471c", "status": "released", "quality_metric": {"status": "released", "uuid": "4db72517-5e8c-44bb-b780-f64c6f0f1897", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/4db72517-5e8c-44bb-b780-f64c6f0f1897/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "21778671", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.223", "tooltip": "Percent of total aligned reads (=0.7m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:54.941378+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P13 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P13", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIX8P1399.bedGraph.gz", "upload_key": "e9b6b04f-a920-4dfc-9d24-2972f9f46b17/4DNFIX8P1399.bedGraph.gz", "href": "/files-processed/4DNFIX8P1399/@@download/4DNFIX8P1399.bedGraph.gz", "accession": "4DNFIX8P1399", "md5sum": "21f77410a27333203d2a7c922b36f49a", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'HnccqeRqTSCCloBWHPyJHA'", "@id": "/files-processed/4DNFIX8P1399/", "file_size": 3854662, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e9b6b04f-a920-4dfc-9d24-2972f9f46b17/4DNFIX8P1399.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "e9b6b04f-a920-4dfc-9d24-2972f9f46b17", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIX8P1399 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P13 of 16 fractions", "@id": "/higlass-view-configs/b5c41609-68c2-4a76-abd2-fbe9a2b6f47f/", "uuid": "b5c41609-68c2-4a76-abd2-fbe9a2b6f47f", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "0e1757dc0797bfdc217456b368bd8cd8", "file_size": 1017306, "href": "/files-processed/4DNFIX8P1399/@@download/4DNFIX8P1399.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "9547ad672ab87eaba4606f4b2d23657a", "file_size": 4396258, "href": "/files-processed/4DNFIX8P1399/@@download/4DNFIX8P1399.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:42.336352+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P13 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P13", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P13 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P13 of 16 fractions", "value": "P13 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:04.524613+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P12 - 4DNEXJ185GTQ", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "dbd144b9-ee0f-4cc9-8368-a121af0bbfce", "accession": "4DNEXJ185GTQ", "files": [{"uuid": "fc3b0740-c719-4110-b19b-c74a225c28fe", "accession": "4DNFI5C3FU8B", "file_classification": "raw file", "display_title": "4DNFI5C3FU8B.fastq.gz", "file_size": 689031148, "href": "/files-fastq/4DNFI5C3FU8B/@@download/4DNFI5C3FU8B.fastq.gz", "md5sum": "242b3242a399504c07030bf146d35ed2", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/fc3b0740-c719-4110-b19b-c74a225c28fe/4DNFI5C3FU8B.fastq.gz", "@id": "/files-fastq/4DNFI5C3FU8B/", "upload_key": "fc3b0740-c719-4110-b19b-c74a225c28fe/4DNFI5C3FU8B.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5C3FU8B/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 14338273, "uuid": "ef12f273-abb6-45ec-9666-8f01e6c6e1e8", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/ef12f273-abb6-45ec-9666-8f01e6c6e1e8/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P12 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P12", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXJ185GTQ/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIF9VHC35.bam", "upload_key": "9a0ea890-00cf-4c15-99e3-e7016e531c19/4DNFIF9VHC35.bam", "href": "/files-processed/4DNFIF9VHC35/@@download/4DNFIF9VHC35.bam", "accession": "4DNFIF9VHC35", "md5sum": "6874d722849e5b53fd57bf9f69c40de2", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIF9VHC35/", "file_size": 670491653, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9a0ea890-00cf-4c15-99e3-e7016e531c19/4DNFIF9VHC35.bam", "file_type_detailed": "alignments (bam)", "uuid": "9a0ea890-00cf-4c15-99e3-e7016e531c19", "status": "released", "quality_metric": {"status": "released", "uuid": "e183b3ed-b72f-4a86-b144-00cb0a4799ef", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/e183b3ed-b72f-4a86-b144-00cb0a4799ef/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "12261050", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "1.877", "tooltip": "Percent of total aligned reads (=0.23m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:03.440337+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P12 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P12", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFITT7ADJ2.bedGraph.gz", "upload_key": "8e00627d-f31e-4e79-a7de-a249b7399818/4DNFITT7ADJ2.bedGraph.gz", "href": "/files-processed/4DNFITT7ADJ2/@@download/4DNFITT7ADJ2.bedGraph.gz", "accession": "4DNFITT7ADJ2", "md5sum": "1300f8e5b6f39f7341e648dc0c75845f", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'bEbrwWXWTNusKbWTBpAk6Q'", "@id": "/files-processed/4DNFITT7ADJ2/", "file_size": 3700106, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8e00627d-f31e-4e79-a7de-a249b7399818/4DNFITT7ADJ2.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "8e00627d-f31e-4e79-a7de-a249b7399818", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFITT7ADJ2 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P12 of 16 fractions", "@id": "/higlass-view-configs/443890f9-7e2f-406c-9a61-1046c0b256eb/", "uuid": "443890f9-7e2f-406c-9a61-1046c0b256eb", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "919496462410676585e75521570548ea", "file_size": 1018497, "href": "/files-processed/4DNFITT7ADJ2/@@download/4DNFITT7ADJ2.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "909690774634b92b4e129ba747c24120", "file_size": 4218511, "href": "/files-processed/4DNFITT7ADJ2/@@download/4DNFITT7ADJ2.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:43.483519+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P12 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P12", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P12 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P12 of 16 fractions", "value": "P12 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:03.448392+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P8 - 4DNEX8K5TT7Y", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "252d7343-7760-40f3-a0eb-52d01ba66b4f", "accession": "4DNEX8K5TT7Y", "files": [{"uuid": "c07d7c83-c789-4e56-a5dd-ddb95701c573", "accession": "4DNFIQ86AI3E", "file_classification": "raw file", "display_title": "4DNFIQ86AI3E.fastq.gz", "file_size": 1613426525, "href": "/files-fastq/4DNFIQ86AI3E/@@download/4DNFIQ86AI3E.fastq.gz", "md5sum": "6acacb624b5afe1abe9d548252e1f543", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c07d7c83-c789-4e56-a5dd-ddb95701c573/4DNFIQ86AI3E.fastq.gz", "@id": "/files-fastq/4DNFIQ86AI3E/", "upload_key": "c07d7c83-c789-4e56-a5dd-ddb95701c573/4DNFIQ86AI3E.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQ86AI3E/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33083681, "uuid": "30ab825f-39c3-4088-be41-132f7cb37dae", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/30ab825f-39c3-4088-be41-132f7cb37dae/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P8 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P08", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX8K5TT7Y/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIKF3BXRX.bam", "upload_key": "f1126d1d-f9f9-420d-883c-e15ea34eb9bd/4DNFIKF3BXRX.bam", "href": "/files-processed/4DNFIKF3BXRX/@@download/4DNFIKF3BXRX.bam", "accession": "4DNFIKF3BXRX", "md5sum": "9e698cd95c6356e17b44e6da829a4b0e", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIKF3BXRX/", "file_size": 1485601586, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f1126d1d-f9f9-420d-883c-e15ea34eb9bd/4DNFIKF3BXRX.bam", "file_type_detailed": "alignments (bam)", "uuid": "f1126d1d-f9f9-420d-883c-e15ea34eb9bd", "status": "released", "quality_metric": {"status": "released", "uuid": "bd67e6fe-9a7a-4885-b4ea-788e494083c1", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/bd67e6fe-9a7a-4885-b4ea-788e494083c1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "27841160", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.585", "tooltip": "Percent of total aligned reads (=1.0m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:46.739811+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P8 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P08", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFILVG2PPB.bedGraph.gz", "upload_key": "6e0c67ab-5830-45d3-a8bb-51f61f25e94b/4DNFILVG2PPB.bedGraph.gz", "href": "/files-processed/4DNFILVG2PPB/@@download/4DNFILVG2PPB.bedGraph.gz", "accession": "4DNFILVG2PPB", "md5sum": "2a587516051c8641194575fb9d6f6e5e", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "TJSP70OjQX2eSJQrTupyFA", "@id": "/files-processed/4DNFILVG2PPB/", "file_size": 3996964, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6e0c67ab-5830-45d3-a8bb-51f61f25e94b/4DNFILVG2PPB.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "6e0c67ab-5830-45d3-a8bb-51f61f25e94b", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFILVG2PPB - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P8 of 16 fractions", "@id": "/higlass-view-configs/ef6c66ed-9239-41f9-85d4-985816323660/", "uuid": "ef6c66ed-9239-41f9-85d4-985816323660", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "5baccc568637ff5d423d42b120a5c48d", "file_size": 1018232, "href": "/files-processed/4DNFILVG2PPB/@@download/4DNFILVG2PPB.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "ef62249e4de70f50a370d6f7047d2ef8", "file_size": 4495589, "href": "/files-processed/4DNFILVG2PPB/@@download/4DNFILVG2PPB.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:44.016704+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P8 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P08", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P8 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P8 of 16 fractions", "value": "P8 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:20.193144+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P17 - 4DNEXKP295JF", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "6fbf5b5b-dedc-447d-b796-d6255a482f3f", "accession": "4DNEXKP295JF", "files": [{"uuid": "655d8789-637a-4cc4-9ad8-d6a20f6e808d", "accession": "4DNFIAM7EBEZ", "file_classification": "raw file", "display_title": "4DNFIAM7EBEZ.fastq.gz", "file_size": 1238221205, "href": "/files-fastq/4DNFIAM7EBEZ/@@download/4DNFIAM7EBEZ.fastq.gz", "md5sum": "59cb82ca68830b52e6c5386d936bdfd8", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/655d8789-637a-4cc4-9ad8-d6a20f6e808d/4DNFIAM7EBEZ.fastq.gz", "@id": "/files-fastq/4DNFIAM7EBEZ/", "upload_key": "655d8789-637a-4cc4-9ad8-d6a20f6e808d/4DNFIAM7EBEZ.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAM7EBEZ/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 25713885, "uuid": "d264f526-c56a-4a41-b1e8-5355fc364616", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/d264f526-c56a-4a41-b1e8-5355fc364616/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P17 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P17", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXKP295JF/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIRAMWYVC.bam", "upload_key": "9a3f3d46-0127-461c-93ff-0204fe9374cc/4DNFIRAMWYVC.bam", "href": "/files-processed/4DNFIRAMWYVC/@@download/4DNFIRAMWYVC.bam", "accession": "4DNFIRAMWYVC", "md5sum": "c9782c5dc02dd622a4ea5896832b0e05", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIRAMWYVC/", "file_size": 737447937, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9a3f3d46-0127-461c-93ff-0204fe9374cc/4DNFIRAMWYVC.bam", "file_type_detailed": "alignments (bam)", "uuid": "9a3f3d46-0127-461c-93ff-0204fe9374cc", "status": "released", "quality_metric": {"status": "released", "uuid": "8f833732-574b-4198-95b9-2d8f16eb3db7", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/8f833732-574b-4198-95b9-2d8f16eb3db7/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "15526344", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "14.912", "tooltip": "Percent of total aligned reads (=2.32m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:19.611271+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P17 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P17", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIEBU9ILY.bedGraph.gz", "upload_key": "467f8574-86f9-42ce-8d37-64a4030b6b44/4DNFIEBU9ILY.bedGraph.gz", "href": "/files-processed/4DNFIEBU9ILY/@@download/4DNFIEBU9ILY.bedGraph.gz", "accession": "4DNFIEBU9ILY", "md5sum": "a3af34f43a7c060478c37300067c97c8", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "K66Ens23TjyCFAQ_6bNkdw", "@id": "/files-processed/4DNFIEBU9ILY/", "file_size": 3697366, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/467f8574-86f9-42ce-8d37-64a4030b6b44/4DNFIEBU9ILY.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "467f8574-86f9-42ce-8d37-64a4030b6b44", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIEBU9ILY - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P17 of 16 fractions", "@id": "/higlass-view-configs/21b90391-0173-4ca6-97e2-093d851dfb73/", "uuid": "21b90391-0173-4ca6-97e2-093d851dfb73", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "56e2f7c642f33e670928c995af93c40a", "file_size": 1016868, "href": "/files-processed/4DNFIEBU9ILY/@@download/4DNFIEBU9ILY.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "111dfafa28f14c44ba3fe68b10a4a4c0", "file_size": 4290725, "href": "/files-processed/4DNFIEBU9ILY/@@download/4DNFIEBU9ILY.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:56.445728+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P17 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P17", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P17 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P17 of 16 fractions", "value": "P17 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:10.061726+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P11 - 4DNEXEYRHQ6L", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "970bcb35-6e9d-4f95-bc0b-97833429fcca", "accession": "4DNEXEYRHQ6L", "files": [{"uuid": "1013c675-98a9-46f4-866c-6c7cdeb6c865", "accession": "4DNFIOVQRRPD", "file_classification": "raw file", "display_title": "4DNFIOVQRRPD.fastq.gz", "file_size": 1054497936, "href": "/files-fastq/4DNFIOVQRRPD/@@download/4DNFIOVQRRPD.fastq.gz", "md5sum": "96c47b2e9c2b0309c2c7692c2d3acf30", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1013c675-98a9-46f4-866c-6c7cdeb6c865/4DNFIOVQRRPD.fastq.gz", "@id": "/files-fastq/4DNFIOVQRRPD/", "upload_key": "1013c675-98a9-46f4-866c-6c7cdeb6c865/4DNFIOVQRRPD.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOVQRRPD/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 21908205, "uuid": "c8305427-40bd-413c-9b89-b6c42c8e9079", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/c8305427-40bd-413c-9b89-b6c42c8e9079/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P11 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P11", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXEYRHQ6L/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIU43BYA9.bam", "upload_key": "000afc02-e1c6-4700-8c06-7ba823357f0b/4DNFIU43BYA9.bam", "href": "/files-processed/4DNFIU43BYA9/@@download/4DNFIU43BYA9.bam", "accession": "4DNFIU43BYA9", "md5sum": "c7b655fa7e29de1764a852909a52a954", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIU43BYA9/", "file_size": 1005598994, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/000afc02-e1c6-4700-8c06-7ba823357f0b/4DNFIU43BYA9.bam", "file_type_detailed": "alignments (bam)", "uuid": "000afc02-e1c6-4700-8c06-7ba823357f0b", "status": "released", "quality_metric": {"status": "released", "uuid": "325f4da3-5fa7-4865-8c8d-65aca705875d", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/325f4da3-5fa7-4865-8c8d-65aca705875d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "18576492", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "2.455", "tooltip": "Percent of total aligned reads (=0.46m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:19.706990+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P11 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P11", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIX7APJSQ.bedGraph.gz", "upload_key": "c3c8b7d4-8bcb-4ac9-a3f3-ba346f9aad43/4DNFIX7APJSQ.bedGraph.gz", "href": "/files-processed/4DNFIX7APJSQ/@@download/4DNFIX7APJSQ.bedGraph.gz", "accession": "4DNFIX7APJSQ", "md5sum": "04cf3595f6ec28ae0c8d4e12e9196354", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'MZJlWM5NRaKx_2MJcmBkvw'", "@id": "/files-processed/4DNFIX7APJSQ/", "file_size": 3850884, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/c3c8b7d4-8bcb-4ac9-a3f3-ba346f9aad43/4DNFIX7APJSQ.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "c3c8b7d4-8bcb-4ac9-a3f3-ba346f9aad43", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIX7APJSQ - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P11 of 16 fractions", "@id": "/higlass-view-configs/5d9de996-829f-4f76-810a-9db86c13a767/", "uuid": "5d9de996-829f-4f76-810a-9db86c13a767", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "dbf763e70666c727b63d32dbb2ce7709", "file_size": 1017846, "href": "/files-processed/4DNFIX7APJSQ/@@download/4DNFIX7APJSQ.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "b32529c78e7cb16d081e4176c5a268c1", "file_size": 4377743, "href": "/files-processed/4DNFIX7APJSQ/@@download/4DNFIX7APJSQ.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:45.214185+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P11 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P11", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P11 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P11 of 16 fractions", "value": "P11 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:02.264090+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P4 - 4DNEX5M9XSGK", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "92304a00-94c9-494d-b80d-90c10fbc4745", "accession": "4DNEX5M9XSGK", "files": [{"uuid": "0480fee5-f2cd-4263-a92a-61b9f4adf3b2", "accession": "4DNFIXB3WDTL", "file_classification": "raw file", "display_title": "4DNFIXB3WDTL.fastq.gz", "file_size": 1865910832, "href": "/files-fastq/4DNFIXB3WDTL/@@download/4DNFIXB3WDTL.fastq.gz", "md5sum": "e6d188d2841b6d58248d6dde2482b993", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0480fee5-f2cd-4263-a92a-61b9f4adf3b2/4DNFIXB3WDTL.fastq.gz", "@id": "/files-fastq/4DNFIXB3WDTL/", "upload_key": "0480fee5-f2cd-4263-a92a-61b9f4adf3b2/4DNFIXB3WDTL.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXB3WDTL/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 38206501, "uuid": "84ba8b66-ef10-4ba5-945b-1915d6fc9f29", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/84ba8b66-ef10-4ba5-945b-1915d6fc9f29/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P4 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P04", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX5M9XSGK/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI37ID2F1.bam", "upload_key": "bd545815-b749-4ed9-b051-b80e5142e6a1/4DNFI37ID2F1.bam", "href": "/files-processed/4DNFI37ID2F1/@@download/4DNFI37ID2F1.bam", "accession": "4DNFI37ID2F1", "md5sum": "34bb3837734dda5b287a6d4535a54f3c", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI37ID2F1/", "file_size": 1652349838, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bd545815-b749-4ed9-b051-b80e5142e6a1/4DNFI37ID2F1.bam", "file_type_detailed": "alignments (bam)", "uuid": "bd545815-b749-4ed9-b051-b80e5142e6a1", "status": "released", "quality_metric": {"status": "released", "uuid": "2b7a3c4b-9220-4c84-97d5-da22f5016b4f", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/2b7a3c4b-9220-4c84-97d5-da22f5016b4f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "31913037", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.835", "tooltip": "Percent of total aligned reads (=1.54m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:39:52.044992+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P4 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P04", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI7GTUE3Q.bedGraph.gz", "upload_key": "efade13a-254a-4d2f-a9e1-922ae01bd707/4DNFI7GTUE3Q.bedGraph.gz", "href": "/files-processed/4DNFI7GTUE3Q/@@download/4DNFI7GTUE3Q.bedGraph.gz", "accession": "4DNFI7GTUE3Q", "md5sum": "c36a996bbe72af475401b8421ecc8357", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "VLE2ksT9SDCceBuxiwgFHA", "@id": "/files-processed/4DNFI7GTUE3Q/", "file_size": 4004923, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/efade13a-254a-4d2f-a9e1-922ae01bd707/4DNFI7GTUE3Q.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "efade13a-254a-4d2f-a9e1-922ae01bd707", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI7GTUE3Q - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P4 of 16 fractions", "@id": "/higlass-view-configs/9914075a-dcf8-42d5-94d2-4e8955130c14/", "uuid": "9914075a-dcf8-42d5-94d2-4e8955130c14", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "fd049bd70caacf6e49701193785fa2ff", "file_size": 1019223, "href": "/files-processed/4DNFI7GTUE3Q/@@download/4DNFI7GTUE3Q.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "3cb7455f0525090d3db7c1affa934a39", "file_size": 4514544, "href": "/files-processed/4DNFI7GTUE3Q/@@download/4DNFI7GTUE3Q.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:39.121618+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P4 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P04", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P4 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P4 of 16 fractions", "value": "P4 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:24.562275+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P10 - 4DNEX8GYBZDB", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "0743117d-d3ee-41fb-9d44-bd1e41ba0a1c", "accession": "4DNEX8GYBZDB", "files": [{"uuid": "c041943f-e9a6-4c07-8425-3c0c03cfdcd3", "accession": "4DNFI5DRLRYM", "file_classification": "raw file", "display_title": "4DNFI5DRLRYM.fastq.gz", "file_size": 757842817, "href": "/files-fastq/4DNFI5DRLRYM/@@download/4DNFI5DRLRYM.fastq.gz", "md5sum": "5770f35fbb1e16ae2e0aa4ab549e3bc8", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c041943f-e9a6-4c07-8425-3c0c03cfdcd3/4DNFI5DRLRYM.fastq.gz", "@id": "/files-fastq/4DNFI5DRLRYM/", "upload_key": "c041943f-e9a6-4c07-8425-3c0c03cfdcd3/4DNFI5DRLRYM.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI5DRLRYM/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 15766430, "uuid": "6a57a1d8-2bc8-41a7-b25b-6a3eae416e27", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/6a57a1d8-2bc8-41a7-b25b-6a3eae416e27/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P10 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P10", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX8GYBZDB/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIDWIV7IR.bam", "upload_key": "31bc1a0e-e81e-42e4-82fd-1a5c7e44d5a7/4DNFIDWIV7IR.bam", "href": "/files-processed/4DNFIDWIV7IR/@@download/4DNFIDWIV7IR.bam", "accession": "4DNFIDWIV7IR", "md5sum": "54bb3e4102776674a9df88471cdb0c42", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIDWIV7IR/", "file_size": 739814374, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/31bc1a0e-e81e-42e4-82fd-1a5c7e44d5a7/4DNFIDWIV7IR.bam", "file_type_detailed": "alignments (bam)", "uuid": "31bc1a0e-e81e-42e4-82fd-1a5c7e44d5a7", "status": "released", "quality_metric": {"status": "released", "uuid": "cae73c76-dc02-48d1-b7fb-50aa43868ad1", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/cae73c76-dc02-48d1-b7fb-50aa43868ad1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "13584628", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "2.289", "tooltip": "Percent of total aligned reads (=0.31m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:28.284061+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P10 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P10", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI29NN6OX.bedGraph.gz", "upload_key": "278388c0-5bd3-42ab-9985-598b2c9b7653/4DNFI29NN6OX.bedGraph.gz", "href": "/files-processed/4DNFI29NN6OX/@@download/4DNFI29NN6OX.bedGraph.gz", "accession": "4DNFI29NN6OX", "md5sum": "4246143eeea77cbb8d3b21ab5bc1fb22", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'dochgDpuSvOTPwYN-96r9w'", "@id": "/files-processed/4DNFI29NN6OX/", "file_size": 3758804, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/278388c0-5bd3-42ab-9985-598b2c9b7653/4DNFI29NN6OX.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "278388c0-5bd3-42ab-9985-598b2c9b7653", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI29NN6OX - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P10 of 16 fractions", "@id": "/higlass-view-configs/d56c6351-2cbf-4640-a23d-4d5181aa8552/", "uuid": "d56c6351-2cbf-4640-a23d-4d5181aa8552", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "3ae8cda471e9aacc71ecb83ab1d90629", "file_size": 1017420, "href": "/files-processed/4DNFI29NN6OX/@@download/4DNFI29NN6OX.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "1494a77034410992a2fd7e3814a98839", "file_size": 4266982, "href": "/files-processed/4DNFI29NN6OX/@@download/4DNFI29NN6OX.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:46.394759+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P10 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P10", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P10 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P10 of 16 fractions", "value": "P10 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:01.061853+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P8 - 4DNEXDNSSMPJ", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "abfd642a-f6af-46c2-99a7-269ff37cde1a", "accession": "4DNEXDNSSMPJ", "files": [{"uuid": "d44353a5-8171-4d4c-b313-72aa955aa6d4", "accession": "4DNFI47CUMPF", "file_classification": "raw file", "display_title": "4DNFI47CUMPF.fastq.gz", "file_size": 714850639, "href": "/files-fastq/4DNFI47CUMPF/@@download/4DNFI47CUMPF.fastq.gz", "md5sum": "50fc7cad6afdcb15d5b94014adaa2e21", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d44353a5-8171-4d4c-b313-72aa955aa6d4/4DNFI47CUMPF.fastq.gz", "@id": "/files-fastq/4DNFI47CUMPF/", "upload_key": "d44353a5-8171-4d4c-b313-72aa955aa6d4/4DNFI47CUMPF.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI47CUMPF/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 14778238, "uuid": "f61864fb-8962-441f-856c-e88d16913669", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/f61864fb-8962-441f-856c-e88d16913669/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P8 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P08", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXDNSSMPJ/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIMH23JF6.bam", "upload_key": "03dea9f6-a917-402e-a729-8e80e681e81e/4DNFIMH23JF6.bam", "href": "/files-processed/4DNFIMH23JF6/@@download/4DNFIMH23JF6.bam", "accession": "4DNFIMH23JF6", "md5sum": "25a87420e531e43c783de091c856366e", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIMH23JF6/", "file_size": 697099704, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/03dea9f6-a917-402e-a729-8e80e681e81e/4DNFIMH23JF6.bam", "file_type_detailed": "alignments (bam)", "uuid": "03dea9f6-a917-402e-a729-8e80e681e81e", "status": "released", "quality_metric": {"status": "released", "uuid": "18be133d-b0fd-4fe6-9c70-7d2a5ba8019c", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/18be133d-b0fd-4fe6-9c70-7d2a5ba8019c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "12630071", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "1.78", "tooltip": "Percent of total aligned reads (=0.22m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:43:04.920878+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P8 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P08", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI8HGPSWR.bedGraph.gz", "upload_key": "890663c6-a018-4668-aa5b-633a234f72da/4DNFI8HGPSWR.bedGraph.gz", "href": "/files-processed/4DNFI8HGPSWR/@@download/4DNFI8HGPSWR.bedGraph.gz", "accession": "4DNFI8HGPSWR", "md5sum": "dd390885b1ea1e046efc4024a58281b7", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'QoxoX7odSUOG-Z1uDoQuMQ'", "@id": "/files-processed/4DNFI8HGPSWR/", "file_size": 3741124, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/890663c6-a018-4668-aa5b-633a234f72da/4DNFI8HGPSWR.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "890663c6-a018-4668-aa5b-633a234f72da", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI8HGPSWR - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P8 of 16 fractions", "@id": "/higlass-view-configs/b830fbf1-192f-4713-bc6b-6857501ad836/", "uuid": "b830fbf1-192f-4713-bc6b-6857501ad836", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "7c645faec5333ef912ac39b689f4532d", "file_size": 1017058, "href": "/files-processed/4DNFI8HGPSWR/@@download/4DNFI8HGPSWR.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "cfbb648fa2aef8223f76039249e34f72", "file_size": 4253138, "href": "/files-processed/4DNFI8HGPSWR/@@download/4DNFI8HGPSWR.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:49.104520+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P8 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P08", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P8 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P8 of 16 fractions", "value": "P8 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:58.383038+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P7 - 4DNEX3WC3JH3", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "d7ff3019-0f39-4505-be46-d2cfcd527dd4", "accession": "4DNEX3WC3JH3", "files": [{"uuid": "38cc4ff8-35c5-4a87-930c-33f8250ad284", "accession": "4DNFI8H92664", "file_classification": "raw file", "display_title": "4DNFI8H92664.fastq.gz", "file_size": 1322870239, "href": "/files-fastq/4DNFI8H92664/@@download/4DNFI8H92664.fastq.gz", "md5sum": "f1b9dbd458c996f9b93bdad4779b2703", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/38cc4ff8-35c5-4a87-930c-33f8250ad284/4DNFI8H92664.fastq.gz", "@id": "/files-fastq/4DNFI8H92664/", "upload_key": "38cc4ff8-35c5-4a87-930c-33f8250ad284/4DNFI8H92664.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8H92664/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 27180870, "uuid": "3b2714ff-7931-47e4-b3b8-ea11884acd34", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/3b2714ff-7931-47e4-b3b8-ea11884acd34/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P7 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P07", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEX3WC3JH3/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIV42DY4S.bam", "upload_key": "514b7be7-b580-4936-a5e7-730208a2617e/4DNFIV42DY4S.bam", "href": "/files-processed/4DNFIV42DY4S/@@download/4DNFIV42DY4S.bam", "accession": "4DNFIV42DY4S", "md5sum": "80e917476d93956e995ac87d835d174d", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIV42DY4S/", "file_size": 1213357386, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/514b7be7-b580-4936-a5e7-730208a2617e/4DNFIV42DY4S.bam", "file_type_detailed": "alignments (bam)", "uuid": "514b7be7-b580-4936-a5e7-730208a2617e", "status": "released", "quality_metric": {"status": "released", "uuid": "f3f7879d-b983-4b10-b9a1-18b07902a0e9", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/f3f7879d-b983-4b10-b9a1-18b07902a0e9/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "22428487", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "2.973", "tooltip": "Percent of total aligned reads (=0.67m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:12.006467+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P7 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P07", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIRW1IUET.bedGraph.gz", "upload_key": "04162ef1-0670-43cc-a2d5-52ffd87b5f5a/4DNFIRW1IUET.bedGraph.gz", "href": "/files-processed/4DNFIRW1IUET/@@download/4DNFIRW1IUET.bedGraph.gz", "accession": "4DNFIRW1IUET", "md5sum": "7da09743ae15fcb983a499789ff03ac3", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'TG_1cBP9RgCbWlaeiBpBww'", "@id": "/files-processed/4DNFIRW1IUET/", "file_size": 3903330, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/04162ef1-0670-43cc-a2d5-52ffd87b5f5a/4DNFIRW1IUET.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "04162ef1-0670-43cc-a2d5-52ffd87b5f5a", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIRW1IUET - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P7 of 16 fractions", "@id": "/higlass-view-configs/418d22bc-0f53-4e12-a56a-39bd15024f51/", "uuid": "418d22bc-0f53-4e12-a56a-39bd15024f51", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "79ccdce494c02c43ed0b3b2fca1b30c4", "file_size": 1017487, "href": "/files-processed/4DNFIRW1IUET/@@download/4DNFIRW1IUET.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "b0fa12b8718b68acc1d849320845c44c", "file_size": 4431629, "href": "/files-processed/4DNFIRW1IUET/@@download/4DNFIRW1IUET.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:50.232557+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P7 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P07", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P7 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P7 of 16 fractions", "value": "P7 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:05:57.355206+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P13 - 4DNEXLVWLA33", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "d2e31e8d-29c8-4bc7-8c76-7a7009e76e76", "accession": "4DNEXLVWLA33", "files": [{"uuid": "97eccf2a-f18e-49ab-bacb-2546c5cdb49e", "accession": "4DNFIWUWCCGM", "file_classification": "raw file", "display_title": "4DNFIWUWCCGM.fastq.gz", "file_size": 1479172100, "href": "/files-fastq/4DNFIWUWCCGM/@@download/4DNFIWUWCCGM.fastq.gz", "md5sum": "ad1015147b9b1f16b990065af031f51d", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/97eccf2a-f18e-49ab-bacb-2546c5cdb49e/4DNFIWUWCCGM.fastq.gz", "@id": "/files-fastq/4DNFIWUWCCGM/", "upload_key": "97eccf2a-f18e-49ab-bacb-2546c5cdb49e/4DNFIWUWCCGM.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWUWCCGM/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 30586494, "uuid": "44a2bbcc-ad6c-4781-b2ea-ad37d6fe3f75", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/44a2bbcc-ad6c-4781-b2ea-ad37d6fe3f75/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P13 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P13", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXLVWLA33/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIE64Y5I7.bam", "upload_key": "17e4fc80-84c7-4e2e-85c1-c19303098b94/4DNFIE64Y5I7.bam", "href": "/files-processed/4DNFIE64Y5I7/@@download/4DNFIE64Y5I7.bam", "accession": "4DNFIE64Y5I7", "md5sum": "3553eafef220b9db335a16d171dcb356", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIE64Y5I7/", "file_size": 1271125923, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/17e4fc80-84c7-4e2e-85c1-c19303098b94/4DNFIE64Y5I7.bam", "file_type_detailed": "alignments (bam)", "uuid": "17e4fc80-84c7-4e2e-85c1-c19303098b94", "status": "released", "quality_metric": {"status": "released", "uuid": "d5fa014d-841f-447a-a8bb-76c7a27f188c", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/d5fa014d-841f-447a-a8bb-76c7a27f188c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "24399307", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "5.286", "tooltip": "Percent of total aligned reads (=1.29m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:42:27.521770+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P13 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P13", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFI2OT3I8S.bedGraph.gz", "upload_key": "ae10d39f-3e9a-4bd2-9477-3a7a3a7c92df/4DNFI2OT3I8S.bedGraph.gz", "href": "/files-processed/4DNFI2OT3I8S/@@download/4DNFI2OT3I8S.bedGraph.gz", "accession": "4DNFI2OT3I8S", "md5sum": "45660bd734323a5fb8ef8d8c6b30e4bd", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "HDUKZMX5REK_bQmh3kLxEQ", "@id": "/files-processed/4DNFI2OT3I8S/", "file_size": 3902259, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ae10d39f-3e9a-4bd2-9477-3a7a3a7c92df/4DNFI2OT3I8S.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "ae10d39f-3e9a-4bd2-9477-3a7a3a7c92df", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFI2OT3I8S - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P13 of 16 fractions", "@id": "/higlass-view-configs/ca526133-3b6f-4504-9268-0bb50a00abd2/", "uuid": "ca526133-3b6f-4504-9268-0bb50a00abd2", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "e80a3fefb680c70605f2cf55381b017e", "file_size": 1018578, "href": "/files-processed/4DNFI2OT3I8S/@@download/4DNFI2OT3I8S.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "d267ee299c7a68f963f26c6eafb43f8d", "file_size": 4423973, "href": "/files-processed/4DNFI2OT3I8S/@@download/4DNFI2OT3I8S.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:51.477885+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P13 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P13", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P13 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P13 of 16 fractions", "value": "P13 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:14.977037+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P17 - 4DNEXO1I4HLD", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "d7b627ba-5fdb-44f3-983f-ccfd2afc963b", "accession": "4DNEXO1I4HLD", "files": [{"uuid": "ea3fd314-5eb4-458e-92ac-5480b692ff45", "accession": "4DNFI13LS6FZ", "file_classification": "raw file", "display_title": "4DNFI13LS6FZ.fastq.gz", "file_size": 1034124100, "href": "/files-fastq/4DNFI13LS6FZ/@@download/4DNFI13LS6FZ.fastq.gz", "md5sum": "bc9be9804f38c42a89d044634772f7cc", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ea3fd314-5eb4-458e-92ac-5480b692ff45/4DNFI13LS6FZ.fastq.gz", "@id": "/files-fastq/4DNFI13LS6FZ/", "upload_key": "ea3fd314-5eb4-458e-92ac-5480b692ff45/4DNFI13LS6FZ.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI13LS6FZ/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 21708467, "uuid": "d0b58e2f-d297-4ed1-9f6f-f875d60cbfa0", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2019-03-27", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/d0b58e2f-d297-4ed1-9f6f-f875d60cbfa0/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P17 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P17", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXO1I4HLD/", "biosample": {"display_title": "4DNBS22OSTAG", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "9968a070-9959-4885-adc7-af743f0f048c", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS22OSTAG", "@id": "/biosamples/4DNBS22OSTAG/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/d629c3fd-4947-4dbd-bd63-fd83ce4a54e8/", "display_title": "BiosampleCellCulture from 2019-03-21", "uuid": "d629c3fd-4947-4dbd-bd63-fd83ce4a54e8", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFI2QDAHS7.bam", "upload_key": "3ab4e8fd-3466-467f-84e3-98b085b308be/4DNFI2QDAHS7.bam", "href": "/files-processed/4DNFI2QDAHS7/@@download/4DNFI2QDAHS7.bam", "accession": "4DNFI2QDAHS7", "md5sum": "a493f9c878dcf0cbb112d3db7ddc2638", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI2QDAHS7/", "file_size": 702510186, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3ab4e8fd-3466-467f-84e3-98b085b308be/4DNFI2QDAHS7.bam", "file_type_detailed": "alignments (bam)", "uuid": "3ab4e8fd-3466-467f-84e3-98b085b308be", "status": "released", "quality_metric": {"status": "released", "uuid": "e650f074-32b9-4da6-a101-12f955cb2ce3", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2019-03-28", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/e650f074-32b9-4da6-a101-12f955cb2ce3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "13999282", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "10.439", "tooltip": "Percent of total aligned reads (=1.46m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:44:33.383704+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P17 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P17", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIH9FEFVO.bedGraph.gz", "upload_key": "9ed61c64-6fc8-4be9-9d35-d89988d561cb/4DNFIH9FEFVO.bedGraph.gz", "href": "/files-processed/4DNFIH9FEFVO/@@download/4DNFIH9FEFVO.bedGraph.gz", "accession": "4DNFIH9FEFVO", "md5sum": "a441312299d6ca6473469fb2d5a446e4", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "b'FgIVrBhoTjWMkXgm7rna1w'", "@id": "/files-processed/4DNFIH9FEFVO/", "file_size": 3659236, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9ed61c64-6fc8-4be9-9d35-d89988d561cb/4DNFIH9FEFVO.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "9ed61c64-6fc8-4be9-9d35-d89988d561cb", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIH9FEFVO - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P17 of 16 fractions", "@id": "/higlass-view-configs/e0b1f984-01ef-4dbf-985d-bacc8465c50d/", "uuid": "e0b1f984-01ef-4dbf-985d-bacc8465c50d", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "876f71e63b3895dd41a41442c10fe4a0", "file_size": 1017005, "href": "/files-processed/4DNFIH9FEFVO/@@download/4DNFIH9FEFVO.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "8f257bafa465b8f1f210542e1724b85c", "file_size": 4269940, "href": "/files-processed/4DNFIH9FEFVO/@@download/4DNFIH9FEFVO.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:54:36.906955+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P17 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P17", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P17 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P17 of 16 fractions", "value": "P17 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:08.874046+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P6 - 4DNEXQ4EXW3K", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "f533fadd-1645-4440-8349-61e83c4e684a", "accession": "4DNEXQ4EXW3K", "files": [{"uuid": "c6b3badc-eeee-43a5-89c7-5fe8bf259185", "accession": "4DNFI1LDK7TI", "file_classification": "raw file", "display_title": "4DNFI1LDK7TI.fastq.gz", "file_size": 1553754275, "href": "/files-fastq/4DNFI1LDK7TI/@@download/4DNFI1LDK7TI.fastq.gz", "md5sum": "21c21af2fdcba67623f007984324f118", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/c6b3badc-eeee-43a5-89c7-5fe8bf259185/4DNFI1LDK7TI.fastq.gz", "@id": "/files-fastq/4DNFI1LDK7TI/", "upload_key": "c6b3badc-eeee-43a5-89c7-5fe8bf259185/4DNFI1LDK7TI.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1LDK7TI/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 31894726, "uuid": "25542fc5-159e-4aec-9fd5-1fddeedd8c89", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/25542fc5-159e-4aec-9fd5-1fddeedd8c89/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P6 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P06", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXQ4EXW3K/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFIKDFHR5X.bam", "upload_key": "ef6d8bea-5ec4-4c99-8520-dee5f76d6a56/4DNFIKDFHR5X.bam", "href": "/files-processed/4DNFIKDFHR5X/@@download/4DNFIKDFHR5X.bam", "accession": "4DNFIKDFHR5X", "md5sum": "8f700aed0e7541f92ade7dbb7922507d", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIKDFHR5X/", "file_size": 1424491863, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ef6d8bea-5ec4-4c99-8520-dee5f76d6a56/4DNFIKDFHR5X.bam", "file_type_detailed": "alignments (bam)", "uuid": "ef6d8bea-5ec4-4c99-8520-dee5f76d6a56", "status": "released", "quality_metric": {"status": "released", "uuid": "6d3b2e5c-a38f-45a2-af7c-86b458e10371", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/6d3b2e5c-a38f-45a2-af7c-86b458e10371/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "26730044", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "3.549", "tooltip": "Percent of total aligned reads (=0.95m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:40:34.795794+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P6 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P06", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIH66G4C7.bedGraph.gz", "upload_key": "62f5ae32-d062-4c96-b2e6-9765d67215cc/4DNFIH66G4C7.bedGraph.gz", "href": "/files-processed/4DNFIH66G4C7/@@download/4DNFIH66G4C7.bedGraph.gz", "accession": "4DNFIH66G4C7", "md5sum": "fcef907ae8ec5e406fea5b03a6aba884", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "fiOQh6L6R_q11idIxZWtYA", "@id": "/files-processed/4DNFIH66G4C7/", "file_size": 3973471, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/62f5ae32-d062-4c96-b2e6-9765d67215cc/4DNFIH66G4C7.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "62f5ae32-d062-4c96-b2e6-9765d67215cc", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIH66G4C7 - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P6 of 16 fractions", "@id": "/higlass-view-configs/5560f7aa-6818-4e63-a23d-a352fea4aa41/", "uuid": "5560f7aa-6818-4e63-a23d-a352fea4aa41", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "01dfc8956ae396a77c05a6abd093d9b1", "file_size": 1018552, "href": "/files-processed/4DNFIH66G4C7/@@download/4DNFIH66G4C7.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "f55f363fd161fafa102bcdad632aa3ff", "file_size": 4475915, "href": "/files-processed/4DNFIH66G4C7/@@download/4DNFIH66G4C7.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:41.380000+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P6 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P06", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P6 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P6 of 16 fractions", "value": "P6 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:22.304843+00:00"}}, {"display_title": "Multi-stage Repli-seq on H1-hESC (Tier 1) S-phase P5 - 4DNEXEQB7RNA", "@type": ["ExperimentRepliseq", "Experiment", "Item"], "status": "released", "uuid": "b60b21f4-7613-4a40-9ad1-e776ca660da0", "accession": "4DNEXEQB7RNA", "files": [{"uuid": "5ca186f2-9ab1-49a4-aad2-7d5824a8767d", "accession": "4DNFIIR6VCUS", "file_classification": "raw file", "display_title": "4DNFIIR6VCUS.fastq.gz", "file_size": 1650343598, "href": "/files-fastq/4DNFIIR6VCUS/@@download/4DNFIIR6VCUS.fastq.gz", "md5sum": "dbebed383e45685c7c46c4963cd51e77", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5ca186f2-9ab1-49a4-aad2-7d5824a8767d/4DNFIIR6VCUS.fastq.gz", "@id": "/files-fastq/4DNFIIR6VCUS/", "upload_key": "5ca186f2-9ab1-49a4-aad2-7d5824a8767d/4DNFIIR6VCUS.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_type": "reads", "file_type_detailed": "reads (fastq)", "extra_files": [], "file_format": {"uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"name": "david-gilbert-lab", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "@id": "/labs/david-gilbert-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIIR6VCUS/fastqc_report.html", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Total Sequences": 33927325, "uuid": "27d61d16-4128-4d1e-b4c8-4979a114a32a", "overall_quality_status": "PASS", "display_title": "QualityMetricFastqc from 2018-02-12", "status": "released", "Sequence length": "50", "@id": "/quality-metrics-fastqc/27d61d16-4128-4d1e-b4c8-4979a114a32a/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "raw file", "assay_info": "P5 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P05", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/experiments-repliseq/4DNEXEQB7RNA/", "biosample": {"display_title": "4DNBS9WYFL4T", "biosample_category": ["H1-hESC", "Human stem cell"], "uuid": "0fd0f43c-15a2-47bf-841e-821a7c2e293a", "modifications_summary": "None", "biosample_type": "stem cells", "accession": "4DNBS9WYFL4T", "@id": "/biosamples/4DNBS9WYFL4T/", "treatments_summary": "None", "status": "released", "biosource_summary": "H1-hESC (Tier 1)", "@type": ["Biosample", "Item"], "biosource": [{"uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "@id": "/biosources/4DNSRV3SKQ8M/", "biosource_type": "stem cell derived cell line", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "accession": "4DNSRV3SKQ8M", "status": "released", "cell_line": {"term_id": "EFO:0003042", "@id": "/ontology-terms/EFO:0003042/", "term_name": "H1-hESC", "preferred_name": "H1-hESC", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "H1-hESC", "synonyms": ["H1"], "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "slim_terms": [{"display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "@type": ["OntologyTerm", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "@type": ["OntologyTerm", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"synonyms": ["animal stem cell"], "status": "released", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "preferred_name": "stem cell", "@id": "/ontology-terms/CL:0000034/", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "display_title": "stem cell", "term_id": "CL:0000034", "slim_terms": [{"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "status": "released", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "modifications": [], "treatments": [], "badges": [{"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "@id": "/badges/gold-biosample/", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "description": "Gold biosample", "title": "Gold Biosample", "badge_classification": "Commendation", "status": "released", "display_title": "Gold Biosample", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "tissue_organ_info": {"tissue_source": "stem cell"}, "cell_culture_details": [{"@id": "/biosample-cell-cultures/ecfb0b5f-9583-499b-831a-18ee1706528b/", "display_title": "BiosampleCellCulture from 2018-02-01", "uuid": "ecfb0b5f-9583-499b-831a-18ee1706528b", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "in_vitro_differentiated": "No", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_classification": "processed file", "file_type": "alignments", "genome_assembly": "GRCh38", "display_title": "4DNFII8Q1YGF.bam", "upload_key": "f6b73681-862b-41a5-9935-9ce3363bd8ae/4DNFII8Q1YGF.bam", "href": "/files-processed/4DNFII8Q1YGF/@@download/4DNFII8Q1YGF.bam", "accession": "4DNFII8Q1YGF", "md5sum": "dfb80b9e85aa95b323bad8025b538a6f", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFII8Q1YGF/", "file_size": 1503059752, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f6b73681-862b-41a5-9935-9ce3363bd8ae/4DNFII8Q1YGF.bam", "file_type_detailed": "alignments (bam)", "uuid": "f6b73681-862b-41a5-9935-9ce3363bd8ae", "status": "released", "quality_metric": {"status": "released", "uuid": "8b4e05c6-e8c0-4928-98b2-44c128886b2e", "@type": ["QualityMetricDedupqcRepliseq", "QualityMetric", "Item"], "display_title": "QualityMetricDedupqcRepliseq from 2018-05-25", "overall_quality_status": "PASS", "@id": "/quality-metrics-dedupqc-repliseq/8b4e05c6-e8c0-4928-98b2-44c128886b2e/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Aligned", "value": "28564620", "numberType": "integer"}, {"title": "Removed Duplicates", "value": "4.34", "tooltip": "Percent of total aligned reads (=1.24m)", "numberType": "percent"}]}, "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-04-14T15:45:19.057324+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P5 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P05", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}}, {"file_classification": "processed file", "file_type": "normalized counts", "genome_assembly": "GRCh38", "display_title": "4DNFIZDXYD2L.bedGraph.gz", "upload_key": "ebdc5b6e-ffeb-4422-9615-35304afbc9fb/4DNFIZDXYD2L.bedGraph.gz", "href": "/files-processed/4DNFIZDXYD2L/@@download/4DNFIZDXYD2L.bedGraph.gz", "accession": "4DNFIZDXYD2L", "md5sum": "23acbd3c74ba76f8590ca3b06c64c2af", "file_format": {"display_title": "bg", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bg/", "status": "released", "uuid": "d1312212-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "higlass_uid": "GxXExBS4QSuEGRQ2bmlZVQ", "@id": "/files-processed/4DNFIZDXYD2L/", "file_size": 3971168, "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ebdc5b6e-ffeb-4422-9615-35304afbc9fb/4DNFIZDXYD2L.bedGraph.gz", "file_type_detailed": "normalized counts (bg)", "uuid": "ebdc5b6e-ffeb-4422-9615-35304afbc9fb", "status": "released", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/jian-ma-lab/", "display_title": "Jian Ma, CMU", "uuid": "040d334a-2872-41ec-a282-53d062044564", "name": "jian-ma-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.040d334a-2872-41ec-a282-53d062044564"]}}, {"@type": ["Lab", "Item"], "status": "current", "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}], "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIZDXYD2L - counts for H1-hESC (Tier 1) Multi-stage Repli-seq P5 of 16 fractions", "@id": "/higlass-view-configs/9966db95-384c-4353-b683-a1e2bbc23d6f/", "uuid": "9966db95-384c-4353-b683-a1e2bbc23d6f", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "extra_files": [{"md5sum": "6f68697069614f8051aa624e38b109ae", "file_size": 1018701, "href": "/files-processed/4DNFIZDXYD2L/@@download/4DNFIZDXYD2L.bedGraph.gz.px2", "file_format": {"display_title": "bg_px2", "uuid": "d1311112-218e-4f61-aaf0-91f226248b2c", "file_format": "bg_px2", "status": "released", "@id": "/file-formats/bg_px2/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"md5sum": "d30af376ebe17966b6029b049d3d0243", "file_size": 4471851, "href": "/files-processed/4DNFIZDXYD2L/@@download/4DNFIZDXYD2L.bw", "use_for": "visualization", "file_format": {"display_title": "bw", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "file_format": "bw", "status": "released", "@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "lab": {"@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2023-10-31T16:58:40.249708+00:00"}, "external_references": [], "track_and_facet_info": {"experimental_lab": "David Gilbert, SDBRI", "experiment_type": "Multi-stage Repli-seq", "experiment_bucket": "processed file", "assay_info": "P5 of 16 fractions", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "P05", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS", "track_title": "normalized counts for H1-hESC (Tier 1) Multi-stage Repli-seq P5 of 16 fractions"}}], "experiment_type": {"uuid": "a81c2c5a-7bec-46cf-ba78-db93fde25ca8", "status": "released", "assay_classification": "Linear DNA Enrichment", "title": "Multi-stage Repli-seq", "assay_subclassification": "Replication Timing", "experiment_category": "Sequencing", "other_tags": ["1D"], "assay_subclass_short": "Replication timing", "display_title": "Multi-stage Repli-seq", "@id": "/experiment-types/multi-stage-repli-seq/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "experiment_categorizer": {"field": "Fraction", "combined": "Fraction: P5 of 16 fractions", "value": "P5 of 16 fractions"}, "last_modified": {"date_modified": "2023-10-04T20:06:23.584847+00:00"}}], "experimentset_type": "custom", "alternate_accessions": ["4DNESL48CTGR"], "other_processed_files": [{"type": "supplementary", "files": [{"file_type_detailed": "initiation zones (txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/17c37f4a-148b-4df6-8659-d04738c6c44d/4DNFI5OBN63G.txt", "file_type": "initiation zones", "@type": ["FileProcessed", "File", "Item"], "file_size": 82431, "md5sum": "497e1bd08977fec77dbbe78df7f6e5fc", "@id": "/files-processed/4DNFI5OBN63G/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI5OBN63G/@@download/4DNFI5OBN63G.txt", "status": "released", "accession": "4DNFI5OBN63G", "uuid": "17c37f4a-148b-4df6-8659-d04738c6c44d", "display_title": "4DNFI5OBN63G.txt", "file_format": {"status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "@id": "/file-formats/txt/", "display_title": "txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@id": "/labs/jennifer-cremins-lab/", "@type": ["Lab", "Item"], "name": "jennifer-cremins-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "track_and_facet_info": {"experiment_type": "Multi-stage Repli-seq", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "All fractions", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "last_modified": {"date_modified": "2022-03-09T22:05:21.349928+00:00"}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "status": "current", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b9cc0275-ff92-4dc2-8972-3c0080d306c4/4DNFI3N8GHKR.txt", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 18553911, "md5sum": "5c33955bac93fc34e68e790aff96f3bc", "@id": "/files-processed/4DNFI3N8GHKR/", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI3N8GHKR/@@download/4DNFI3N8GHKR.txt", "status": "released", "accession": "4DNFI3N8GHKR", "uuid": "b9cc0275-ff92-4dc2-8972-3c0080d306c4", "display_title": "4DNFI3N8GHKR.txt", "file_format": {"status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "@id": "/file-formats/txt/", "display_title": "txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"status": "current", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@id": "/labs/jennifer-cremins-lab/", "@type": ["Lab", "Item"], "name": "jennifer-cremins-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "track_and_facet_info": {"experiment_type": "Multi-stage Repli-seq", "dataset": "16-fraction Repli-seq on H1-hESC", "condition": "All fractions", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "David Gilbert, SDBRI"}, "last_modified": {"date_modified": "2022-03-09T22:05:19.850564+00:00"}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/david-gilbert-lab/", "display_title": "David Gilbert, SDBRI", "uuid": "6423b207-8176-4f06-a127-951b98d6a53a", "status": "current", "name": "david-gilbert-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6423b207-8176-4f06-a127-951b98d6a53a"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "normalized counts (txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a7331d35-717e-4d0e-9cdc-357644b9a3d4/4DNFIEEYFQ7C.txt", "file_type": "normalized counts", "@type": ["FileProcessed", "File", "Item"], "file_size": 15451399, "md5sum": "1db0739c62ea7be8af3ad70337517bbf", "@id": "/files-processed/4DNFIEEYFQ7C/", "href": "/files-processed/4DNFIEEYFQ7C/@@download/4DNFIEEYFQ7C.txt", "status": "released", "accession": "4DNFIEEYFQ7C", "uuid": "a7331d35-717e-4d0e-9cdc-357644b9a3d4", "display_title": "4DNFIEEYFQ7C.txt", "file_format": {"status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "@id": "/file-formats/txt/", "display_title": "txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"lab_name": "Jennifer Cremins, UPENN"}, "last_modified": {"date_modified": "2022-05-03T21:33:53.579292+00:00"}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "status": "current", "name": "jennifer-cremins-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "initiation zones (txt)", "genome_assembly": "GRCh38", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ad47c638-be39-46e4-860b-91116d789ce5/4DNFIRF7WZ3H.txt", "file_type": "initiation zones", "@type": ["FileProcessed", "File", "Item"], "file_size": 102775, "md5sum": "7fa7d9d7a55cb2c19933ade6de16093d", "@id": "/files-processed/4DNFIRF7WZ3H/", "href": "/files-processed/4DNFIRF7WZ3H/@@download/4DNFIRF7WZ3H.txt", "status": "released", "accession": "4DNFIRF7WZ3H", "uuid": "ad47c638-be39-46e4-860b-91116d789ce5", "display_title": "4DNFIRF7WZ3H.txt", "file_format": {"status": "released", "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "@id": "/file-formats/txt/", "display_title": "txt", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"lab_name": "Jennifer Cremins, UPENN"}, "last_modified": {"date_modified": "2022-05-03T21:33:55.459293+00:00"}, "lab": {"@type": ["Lab", "Item"], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "status": "current", "name": "jennifer-cremins-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "HiRes Repli-seq arrays and IZ calls - Gilbert Lab", "description": "Normalized count arrays from HiRes Repli-seq and Initiation Zone Calls generated using the normalized arrays provided by the data producing lab"}], "@id": "/experiment-sets/4DNESXRBILXJ/", "@type": ["ExperimentSet", "Item"], "uuid": "2dc82177-cb40-4de6-b029-745d9ecd5a54", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESXRBILXJ", "external_references": [], "produced_in_pub": {"url": "https://www.ncbi.nlm.nih.gov/pubmed/32209126", "@id": "/publications/7f3c096b-38fc-4fc1-abf8-679e8d90e9dd/", "short_attribution": "Zhao PA et al. (2020)", "ID": "PMID:32209126", "journal": "Genome biology", "uuid": "7f3c096b-38fc-4fc1-abf8-679e8d90e9dd", "abstract": "BACKGROUND: DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here, we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116, and mouse embryonic stem cells and their neural progenitor derivatives. RESULTS: Fine temporal windows revealed a remarkable degree of cell-to-cell conservation in RT, particularly at the very beginning and ends of S phase, and identified 5 temporal patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation (IZs) were detected throughout S phase and interacted in 3D space preferentially with other IZs of similar firing time. Temporal transition regions were resolved into segments of uni-directional replication punctuated at specific sites by small, inefficient IZs. Sites of convergent replication were divided into sites of termination or large constant timing regions consisting of many synchronous IZs in tandem. Developmental transitions in RT occured mainly by activating or inactivating individual IZs or occasionally by altering IZ firing time, demonstrating that IZs, rather than individual origins, are the units of developmental regulation. Finally, haplotype phasing revealed numerous regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchronous replication was correlated with the presence of previously mapped common fragile sites. CONCLUSIONS: Altogether, these data provide a detailed temporal choreography of DNA replication in mammalian cells.", "authors": ["Zhao PA", "Sasaki T", "Gilbert DM"], "date_published": "2020-03-24", "@type": ["Publication", "Item"], "display_title": "Zhao PA et al. (2020) PMID:32209126", "status": "current", "title": "High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"date_published": "2020-03-24", "ID": "PMID:32209126", "status": "current", "authors": ["Zhao PA", "Sasaki T", "Gilbert DM"], "@id": "/publications/7f3c096b-38fc-4fc1-abf8-679e8d90e9dd/", "abstract": "BACKGROUND: DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here, we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116, and mouse embryonic stem cells and their neural progenitor derivatives. RESULTS: Fine temporal windows revealed a remarkable degree of cell-to-cell conservation in RT, particularly at the very beginning and ends of S phase, and identified 5 temporal patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation (IZs) were detected throughout S phase and interacted in 3D space preferentially with other IZs of similar firing time. Temporal transition regions were resolved into segments of uni-directional replication punctuated at specific sites by small, inefficient IZs. Sites of convergent replication were divided into sites of termination or large constant timing regions consisting of many synchronous IZs in tandem. Developmental transitions in RT occured mainly by activating or inactivating individual IZs or occasionally by altering IZ firing time, demonstrating that IZs, rather than individual origins, are the units of developmental regulation. Finally, haplotype phasing revealed numerous regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchronous replication was correlated with the presence of previously mapped common fragile sites. CONCLUSIONS: Altogether, these data provide a detailed temporal choreography of DNA replication in mammalian cells.", "@type": ["Publication", "Item"], "title": "High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells.", "journal": "Genome biology", "display_title": "Zhao PA et al. (2020) PMID:32209126", "uuid": "7f3c096b-38fc-4fc1-abf8-679e8d90e9dd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 34, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS22OSTAG/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}, {"parent": "/biosamples/4DNBS9WYFL4T/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}]}, "validation-errors": []}