{"lab": {"status": "current", "@type": ["Lab", "Item"], "title": "Kikue Tachibana, IMBA", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "award": {"@id": "/awards/1U54DK107980-01/", "uuid": "ae6c618f-7a8c-441e-a886-e30bbbe591da", "description": "NOFIC: The spatial organization of the genome impinges on all genomic processes, including gene regulation, maintenance of genome stability and chromosome transmission to daughter cells. A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. Effects of such perturbations in the chromosome conformation on transcription will reveal relationships between specific chromosome structural features and gene expression.", "name": "1U54DK107980-01", "center_title": "NOFIC - Dekker", "project": "4DN", "display_title": "CENTER FOR 3D STRUCTURE AND PHYSICS OF THE GENOME", "@type": ["Award", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["mirny-lab:repset_pat_scc1_control"], "dbxrefs": ["GEO:GSE100569"], "accession": "4DNESTRAR8I6", "description": "single nucleus Hi-C on paternal pronuclei from Scc1 control", "date_created": "2018-06-22T17:38:00.284209+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-06-12T17:26:16.315591+00:00"}, "public_release": "2018-08-30", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXCRPONJK", "uuid": "09fdf10b-10f7-4e9d-8e11-9011f61ccc8a", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXCRPONJK", "@id": "/experiments-hi-c/4DNEXCRPONJK/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXKNJ8IZL", "uuid": "a1d09d46-5220-488b-8dee-c868b90f050f", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXKNJ8IZL", "@id": "/experiments-hi-c/4DNEXKNJ8IZL/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXMQQLXEF", "uuid": "cea9a65f-15cb-4bcf-942c-889c86e4970d", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXMQQLXEF", "@id": "/experiments-hi-c/4DNEXMQQLXEF/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXYY99BC1", "uuid": "bbd5e62c-0145-47a6-ac99-072915737e07", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXYY99BC1", "@id": "/experiments-hi-c/4DNEXYY99BC1/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 5, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXG1E8VIB", "uuid": "db0ee109-1aa0-4a6f-82de-f61838535ac9", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXG1E8VIB", "@id": "/experiments-hi-c/4DNEXG1E8VIB/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 6, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXNG723W7", "uuid": "6fa34f18-ac85-48e1-ab7e-999fcb45423b", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXNG723W7", "@id": "/experiments-hi-c/4DNEXNG723W7/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 7, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXVYPFU2Z", "uuid": "19e07a6b-ba6f-4712-917d-32d2111c9c24", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXVYPFU2Z", "@id": "/experiments-hi-c/4DNEXVYPFU2Z/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 8, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEX4WH19KC", "uuid": "249e8d6b-8312-45b2-82af-b40ed1c24399", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX4WH19KC", "@id": "/experiments-hi-c/4DNEX4WH19KC/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 9, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXS6OQK33", "uuid": "3bb694b4-72cf-49fe-85d1-6fcbf07175ea", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXS6OQK33", "@id": "/experiments-hi-c/4DNEXS6OQK33/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 10, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXKBWQZWV", "uuid": "59066e6a-2150-4386-9377-d2ed329ce457", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXKBWQZWV", "@id": "/experiments-hi-c/4DNEXKBWQZWV/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 11, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXTQ2S37G", "uuid": "c95fd0ca-b176-49e7-9a83-04136815e9b9", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXTQ2S37G", "@id": "/experiments-hi-c/4DNEXTQ2S37G/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 12, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXJG7S766", "uuid": "f81285c6-c56d-43b9-baa8-8826c329bd9a", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXJG7S766", "@id": "/experiments-hi-c/4DNEXJG7S766/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 13, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXZIJQ1QD", "uuid": "ac067405-296a-4842-ba3c-7ce0d604057e", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXZIJQ1QD", "@id": "/experiments-hi-c/4DNEXZIJQ1QD/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 14, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXB8X9LR4", "uuid": "1cd4dffc-a650-43a0-b244-b81ee6ad5ae6", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXB8X9LR4", "@id": "/experiments-hi-c/4DNEXB8X9LR4/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 15, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXYD9WRE2", "uuid": "1b9b4101-5e76-4d74-976b-928c94aa1487", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXYD9WRE2", "@id": "/experiments-hi-c/4DNEXYD9WRE2/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 16, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEX1YNIZLY", "uuid": "d0450986-0142-4f3a-8b35-be636509c8f2", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX1YNIZLY", "@id": "/experiments-hi-c/4DNEX1YNIZLY/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 17, "tec_rep_no": 1, "replicate_exp": {"display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEX55MBKJJ", "uuid": "500c6289-4d10-42f3-9363-4b82f7ee94eb", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX55MBKJJ", "@id": "/experiments-hi-c/4DNEX55MBKJJ/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "project_release": "2018-08-30", "contributing_labs": [{"correspondence": [{"contact_email": "bGVvbmlkQG1pdC5lZHU=", "@id": "/users/f520d12a-e4c4-4774-a230-08d6dc4f5ef1/", "display_title": "Leonid Mirny"}], "display_title": "Leonid Mirny, MIT", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "experiments_in_set": [{"dbxrefs": ["SRA:SRX2961710"], "status": "released", "@id": "/experiments-hi-c/4DNEXCRPONJK/", "files": [{"file_size": 1270325896, "@type": ["FileFastq", "File", "Item"], "upload_key": "72427fe6-d121-47af-903f-9d5467b16ba9/4DNFITFIPTJY.fastq.gz", "@id": "/files-fastq/4DNFITFIPTJY/", "md5sum": "f3f99ceded98224ddd52ccbf781bfe08", "uuid": "72427fe6-d121-47af-903f-9d5467b16ba9", "paired_end": "1", "file_type": "reads", "display_title": "4DNFITFIPTJY.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/72427fe6-d121-47af-903f-9d5467b16ba9/4DNFITFIPTJY.fastq.gz", "accession": "4DNFITFIPTJY", "href": "/files-fastq/4DNFITFIPTJY/@@download/4DNFITFIPTJY.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIU77QYWO/", "paired_end": "2", "uuid": "4f139f5d-2cc1-46bd-a153-ba1c87e623ff", "display_title": "4DNFIU77QYWO.fastq.gz", "accession": "4DNFIU77QYWO", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/d9ca88be-12c8-4351-9629-f1dff4117ed7/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "d9ca88be-12c8-4351-9629-f1dff4117ed7", "Total Sequences": 18402915, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITFIPTJY/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1303520808, "@type": ["FileFastq", "File", "Item"], "upload_key": "4f139f5d-2cc1-46bd-a153-ba1c87e623ff/4DNFIU77QYWO.fastq.gz", "@id": "/files-fastq/4DNFIU77QYWO/", "md5sum": "74b24b97d381101eff1371862e103b59", "uuid": "4f139f5d-2cc1-46bd-a153-ba1c87e623ff", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIU77QYWO.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4f139f5d-2cc1-46bd-a153-ba1c87e623ff/4DNFIU77QYWO.fastq.gz", "accession": "4DNFIU77QYWO", "href": "/files-fastq/4DNFIU77QYWO/@@download/4DNFIU77QYWO.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITFIPTJY/", "paired_end": "1", "uuid": "72427fe6-d121-47af-903f-9d5467b16ba9", "display_title": "4DNFITFIPTJY.fastq.gz", "accession": "4DNFITFIPTJY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/e0d4e0f4-4f2c-4adf-acfb-0bef0902a952/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "e0d4e0f4-4f2c-4adf-acfb-0bef0902a952", "Total Sequences": 18402915, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIU77QYWO/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "09fdf10b-10f7-4e9d-8e11-9011f61ccc8a", "accession": "4DNEXCRPONJK", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXCRPONJK", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSWIOAS2B", "@id": "/biosamples/4DNBSWIOAS2B/", "biosample_category": ["Primary Cells"], "uuid": "939aac27-1c82-4f50-8e6b-980cf1f80a07", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSWIOAS2B", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:31.674319+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961710", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961710"}]}, {"dbxrefs": ["SRA:SRX2961712"], "status": "released", "@id": "/experiments-hi-c/4DNEXKNJ8IZL/", "files": [{"file_size": 1208716092, "@type": ["FileFastq", "File", "Item"], "upload_key": "ea631fbb-e3b3-4daa-a6f5-aa6aae2cae0c/4DNFIUMKX57U.fastq.gz", "@id": "/files-fastq/4DNFIUMKX57U/", "md5sum": "94aa9713284a24a2cf7997ae8c152051", "uuid": "ea631fbb-e3b3-4daa-a6f5-aa6aae2cae0c", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIUMKX57U.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/ea631fbb-e3b3-4daa-a6f5-aa6aae2cae0c/4DNFIUMKX57U.fastq.gz", "accession": "4DNFIUMKX57U", "href": "/files-fastq/4DNFIUMKX57U/@@download/4DNFIUMKX57U.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI7L2WPYL/", "paired_end": "2", "uuid": "a4316d38-052d-4e88-a377-c71c04de1ff3", "display_title": "4DNFI7L2WPYL.fastq.gz", "accession": "4DNFI7L2WPYL", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/600eb844-d056-4e22-bdcb-f9c455dd4926/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "600eb844-d056-4e22-bdcb-f9c455dd4926", "Total Sequences": 17762828, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUMKX57U/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1235320596, "@type": ["FileFastq", "File", "Item"], "upload_key": "a4316d38-052d-4e88-a377-c71c04de1ff3/4DNFI7L2WPYL.fastq.gz", "@id": "/files-fastq/4DNFI7L2WPYL/", "md5sum": "00de87f584d1c6b65035fb3730192006", "uuid": "a4316d38-052d-4e88-a377-c71c04de1ff3", "paired_end": "2", "file_type": "reads", "display_title": "4DNFI7L2WPYL.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a4316d38-052d-4e88-a377-c71c04de1ff3/4DNFI7L2WPYL.fastq.gz", "accession": "4DNFI7L2WPYL", "href": "/files-fastq/4DNFI7L2WPYL/@@download/4DNFI7L2WPYL.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIUMKX57U/", "paired_end": "1", "uuid": "ea631fbb-e3b3-4daa-a6f5-aa6aae2cae0c", "display_title": "4DNFIUMKX57U.fastq.gz", "accession": "4DNFIUMKX57U", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/5648ca15-0691-4c07-b958-8b7588c82aa2/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "5648ca15-0691-4c07-b958-8b7588c82aa2", "Total Sequences": 17762828, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7L2WPYL/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "a1d09d46-5220-488b-8dee-c868b90f050f", "accession": "4DNEXKNJ8IZL", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXKNJ8IZL", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSAR91369", "@id": "/biosamples/4DNBSAR91369/", "biosample_category": ["Primary Cells"], "uuid": "0c60c879-75e7-4dc4-a8c1-e8978525c35a", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSAR91369", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:32:48.654815+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961712", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961712"}]}, {"dbxrefs": ["SRA:SRX2961713"], "status": "released", "@id": "/experiments-hi-c/4DNEXMQQLXEF/", "files": [{"file_size": 1021507113, "@type": ["FileFastq", "File", "Item"], "upload_key": "094c3764-eaef-4eda-a5fb-146f99de12cf/4DNFIN5271R8.fastq.gz", "@id": "/files-fastq/4DNFIN5271R8/", "md5sum": "e92a1b929a547400de66c5aa9a07168c", "uuid": "094c3764-eaef-4eda-a5fb-146f99de12cf", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIN5271R8.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/094c3764-eaef-4eda-a5fb-146f99de12cf/4DNFIN5271R8.fastq.gz", "accession": "4DNFIN5271R8", "href": "/files-fastq/4DNFIN5271R8/@@download/4DNFIN5271R8.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIGZD35TU/", "paired_end": "2", "uuid": "484abd34-1a8b-41b0-9aa9-3b026d8426a7", "display_title": "4DNFIGZD35TU.fastq.gz", "accession": "4DNFIGZD35TU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/9c656310-5b28-42ed-bbd2-c6d805fb5400/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "9c656310-5b28-42ed-bbd2-c6d805fb5400", "Total Sequences": 14757936, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIN5271R8/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1043422558, "@type": ["FileFastq", "File", "Item"], "upload_key": "484abd34-1a8b-41b0-9aa9-3b026d8426a7/4DNFIGZD35TU.fastq.gz", "@id": "/files-fastq/4DNFIGZD35TU/", "md5sum": "fb32ac5222ae2e13616e0b2e78b1104d", "uuid": "484abd34-1a8b-41b0-9aa9-3b026d8426a7", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIGZD35TU.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/484abd34-1a8b-41b0-9aa9-3b026d8426a7/4DNFIGZD35TU.fastq.gz", "accession": "4DNFIGZD35TU", "href": "/files-fastq/4DNFIGZD35TU/@@download/4DNFIGZD35TU.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIN5271R8/", "paired_end": "1", "uuid": "094c3764-eaef-4eda-a5fb-146f99de12cf", "display_title": "4DNFIN5271R8.fastq.gz", "accession": "4DNFIN5271R8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/beb0b16f-1785-4a44-b68e-a6e6065cac5c/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "beb0b16f-1785-4a44-b68e-a6e6065cac5c", "Total Sequences": 14757936, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGZD35TU/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "cea9a65f-15cb-4bcf-942c-889c86e4970d", "accession": "4DNEXMQQLXEF", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXMQQLXEF", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSO7KF2AP", "@id": "/biosamples/4DNBSO7KF2AP/", "biosample_category": ["Primary Cells"], "uuid": "1106ce7b-ff89-4950-9ccd-f14a8940f1a7", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSO7KF2AP", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:32:38.719473+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961713", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961713"}]}, {"dbxrefs": ["SRA:SRX2961714"], "status": "released", "@id": "/experiments-hi-c/4DNEXYY99BC1/", "files": [{"file_size": 918655399, "@type": ["FileFastq", "File", "Item"], "upload_key": "cd5f4f36-792a-43bd-a12a-73da09f6ad38/4DNFII4LEB62.fastq.gz", "@id": "/files-fastq/4DNFII4LEB62/", "md5sum": "7f6a0b644255f720b491c9cd4364be2b", "uuid": "cd5f4f36-792a-43bd-a12a-73da09f6ad38", "paired_end": "1", "file_type": "reads", "display_title": "4DNFII4LEB62.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/cd5f4f36-792a-43bd-a12a-73da09f6ad38/4DNFII4LEB62.fastq.gz", "accession": "4DNFII4LEB62", "href": "/files-fastq/4DNFII4LEB62/@@download/4DNFII4LEB62.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFICH1JGZD/", "paired_end": "2", "uuid": "b5354211-d90e-4b31-9795-0b914e24e85f", "display_title": "4DNFICH1JGZD.fastq.gz", "accession": "4DNFICH1JGZD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/64c1acf1-d255-419b-b85d-291569099f05/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "64c1acf1-d255-419b-b85d-291569099f05", "Total Sequences": 13732664, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFII4LEB62/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 929853648, "@type": ["FileFastq", "File", "Item"], "upload_key": "b5354211-d90e-4b31-9795-0b914e24e85f/4DNFICH1JGZD.fastq.gz", "@id": "/files-fastq/4DNFICH1JGZD/", "md5sum": "5836d72d6c8c8c608b55a02981e8090a", "uuid": "b5354211-d90e-4b31-9795-0b914e24e85f", "paired_end": "2", "file_type": "reads", "display_title": "4DNFICH1JGZD.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b5354211-d90e-4b31-9795-0b914e24e85f/4DNFICH1JGZD.fastq.gz", "accession": "4DNFICH1JGZD", "href": "/files-fastq/4DNFICH1JGZD/@@download/4DNFICH1JGZD.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFII4LEB62/", "paired_end": "1", "uuid": "cd5f4f36-792a-43bd-a12a-73da09f6ad38", "display_title": "4DNFII4LEB62.fastq.gz", "accession": "4DNFII4LEB62", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/42583243-9a68-4d9f-a0f0-c98339c4e0a4/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "42583243-9a68-4d9f-a0f0-c98339c4e0a4", "Total Sequences": 13732664, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICH1JGZD/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "bbd5e62c-0145-47a6-ac99-072915737e07", "accession": "4DNEXYY99BC1", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXYY99BC1", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSCOALVK9", "@id": "/biosamples/4DNBSCOALVK9/", "biosample_category": ["Primary Cells"], "uuid": "668649ab-3841-4464-aeec-2666aed09d40", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSCOALVK9", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:32:44.291833+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961714", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961714"}]}, {"dbxrefs": ["SRA:SRX2961715"], "status": "released", "@id": "/experiments-hi-c/4DNEXG1E8VIB/", "files": [{"file_size": 1179544395, "@type": ["FileFastq", "File", "Item"], "upload_key": "02acce86-daed-42cc-a031-fde27508ad27/4DNFIP7ZHXQJ.fastq.gz", "@id": "/files-fastq/4DNFIP7ZHXQJ/", "md5sum": "e8450e19539863a68988b896e96b881a", "uuid": "02acce86-daed-42cc-a031-fde27508ad27", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIP7ZHXQJ.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/02acce86-daed-42cc-a031-fde27508ad27/4DNFIP7ZHXQJ.fastq.gz", "accession": "4DNFIP7ZHXQJ", "href": "/files-fastq/4DNFIP7ZHXQJ/@@download/4DNFIP7ZHXQJ.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIKYI954T/", "paired_end": "2", "uuid": "03035864-65f1-4cab-a644-6d30d2614f80", "display_title": "4DNFIKYI954T.fastq.gz", "accession": "4DNFIKYI954T", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/e12b980a-29da-449a-89c2-ca3912920130/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "e12b980a-29da-449a-89c2-ca3912920130", "Total Sequences": 17833096, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIP7ZHXQJ/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 5, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1204201249, "@type": ["FileFastq", "File", "Item"], "upload_key": "03035864-65f1-4cab-a644-6d30d2614f80/4DNFIKYI954T.fastq.gz", "@id": "/files-fastq/4DNFIKYI954T/", "md5sum": "8d653a3c1ce3d1129c492b4460fcd0c1", "uuid": "03035864-65f1-4cab-a644-6d30d2614f80", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIKYI954T.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/03035864-65f1-4cab-a644-6d30d2614f80/4DNFIKYI954T.fastq.gz", "accession": "4DNFIKYI954T", "href": "/files-fastq/4DNFIKYI954T/@@download/4DNFIKYI954T.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIP7ZHXQJ/", "paired_end": "1", "uuid": "02acce86-daed-42cc-a031-fde27508ad27", "display_title": "4DNFIP7ZHXQJ.fastq.gz", "accession": "4DNFIP7ZHXQJ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/d3643352-f626-4a97-828e-8e3160a078eb/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "d3643352-f626-4a97-828e-8e3160a078eb", "Total Sequences": 17833096, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKYI954T/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 5, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "db0ee109-1aa0-4a6f-82de-f61838535ac9", "accession": "4DNEXG1E8VIB", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXG1E8VIB", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSYE67WNA", "@id": "/biosamples/4DNBSYE67WNA/", "biosample_category": ["Primary Cells"], "uuid": "efa72ea0-0e00-4e5a-a308-4bdd7c6d70bc", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSYE67WNA", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:35.292282+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961715", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961715"}]}, {"dbxrefs": ["SRA:SRX2961717"], "status": "released", "@id": "/experiments-hi-c/4DNEXNG723W7/", "files": [{"file_size": 868777842, "@type": ["FileFastq", "File", "Item"], "upload_key": "b171506a-6f53-451d-9bbb-2a71b2a4ec8e/4DNFI1Q1RYOR.fastq.gz", "@id": "/files-fastq/4DNFI1Q1RYOR/", "md5sum": "3cff6104c4b5a929ad9a0233072b28f6", "uuid": "b171506a-6f53-451d-9bbb-2a71b2a4ec8e", "paired_end": "1", "file_type": "reads", "display_title": "4DNFI1Q1RYOR.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b171506a-6f53-451d-9bbb-2a71b2a4ec8e/4DNFI1Q1RYOR.fastq.gz", "accession": "4DNFI1Q1RYOR", "href": "/files-fastq/4DNFI1Q1RYOR/@@download/4DNFI1Q1RYOR.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFICMORDZM/", "paired_end": "2", "uuid": "1403c740-a132-4f07-a888-d7d0621abd10", "display_title": "4DNFICMORDZM.fastq.gz", "accession": "4DNFICMORDZM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/4410be08-d820-4615-bc23-9978b6ed6d4a/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "4410be08-d820-4615-bc23-9978b6ed6d4a", "Total Sequences": 12792453, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1Q1RYOR/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 6, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 879358116, "@type": ["FileFastq", "File", "Item"], "upload_key": "1403c740-a132-4f07-a888-d7d0621abd10/4DNFICMORDZM.fastq.gz", "@id": "/files-fastq/4DNFICMORDZM/", "md5sum": "bc3a28801f6ea8c2db831141aaf9056f", "uuid": "1403c740-a132-4f07-a888-d7d0621abd10", "paired_end": "2", "file_type": "reads", "display_title": "4DNFICMORDZM.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1403c740-a132-4f07-a888-d7d0621abd10/4DNFICMORDZM.fastq.gz", "accession": "4DNFICMORDZM", "href": "/files-fastq/4DNFICMORDZM/@@download/4DNFICMORDZM.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI1Q1RYOR/", "paired_end": "1", "uuid": "b171506a-6f53-451d-9bbb-2a71b2a4ec8e", "display_title": "4DNFI1Q1RYOR.fastq.gz", "accession": "4DNFI1Q1RYOR", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/2c7cc46d-6e18-4718-9849-0a76137d741a/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "2c7cc46d-6e18-4718-9849-0a76137d741a", "Total Sequences": 12792453, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICMORDZM/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 6, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "6fa34f18-ac85-48e1-ab7e-999fcb45423b", "accession": "4DNEXNG723W7", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXNG723W7", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSTZYWFWH", "@id": "/biosamples/4DNBSTZYWFWH/", "biosample_category": ["Primary Cells"], "uuid": "81f0bf0c-14ff-417a-a4ff-f84b4fd57756", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSTZYWFWH", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:00.128358+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961717", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961717"}]}, {"dbxrefs": ["SRA:SRX2961759"], "status": "released", "@id": "/experiments-hi-c/4DNEXVYPFU2Z/", "files": [{"file_size": 1468491892, "@type": ["FileFastq", "File", "Item"], "upload_key": "749388ac-f7e7-416b-9939-a1f845a648dd/4DNFIGDDSWB9.fastq.gz", "@id": "/files-fastq/4DNFIGDDSWB9/", "md5sum": "81770c899a42b4fcf1370e0cec24148b", "uuid": "749388ac-f7e7-416b-9939-a1f845a648dd", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIGDDSWB9.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/749388ac-f7e7-416b-9939-a1f845a648dd/4DNFIGDDSWB9.fastq.gz", "accession": "4DNFIGDDSWB9", "href": "/files-fastq/4DNFIGDDSWB9/@@download/4DNFIGDDSWB9.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIYQTSJYZ/", "paired_end": "2", "uuid": "4150bec4-0ed6-4dea-b0e7-899ddf4296b0", "display_title": "4DNFIYQTSJYZ.fastq.gz", "accession": "4DNFIYQTSJYZ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/7bf7e2ee-fc06-498e-bd02-4b482f8a9a5c/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "7bf7e2ee-fc06-498e-bd02-4b482f8a9a5c", "Total Sequences": 21112230, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-18", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGDDSWB9/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 7, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1505299906, "@type": ["FileFastq", "File", "Item"], "upload_key": "4150bec4-0ed6-4dea-b0e7-899ddf4296b0/4DNFIYQTSJYZ.fastq.gz", "@id": "/files-fastq/4DNFIYQTSJYZ/", "md5sum": "73823c905796ff9e5a40b1e59ba6a279", "uuid": "4150bec4-0ed6-4dea-b0e7-899ddf4296b0", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIYQTSJYZ.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4150bec4-0ed6-4dea-b0e7-899ddf4296b0/4DNFIYQTSJYZ.fastq.gz", "accession": "4DNFIYQTSJYZ", "href": "/files-fastq/4DNFIYQTSJYZ/@@download/4DNFIYQTSJYZ.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIGDDSWB9/", "paired_end": "1", "uuid": "749388ac-f7e7-416b-9939-a1f845a648dd", "display_title": "4DNFIGDDSWB9.fastq.gz", "accession": "4DNFIGDDSWB9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/ca78a2b4-8935-4bd6-b6b1-b7844141508f/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "ca78a2b4-8935-4bd6-b6b1-b7844141508f", "Total Sequences": 21112230, "status": "released", "display_title": "QualityMetricFastqc from 2018-06-19", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIYQTSJYZ/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 7, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "19e07a6b-ba6f-4712-917d-32d2111c9c24", "accession": "4DNEXVYPFU2Z", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXVYPFU2Z", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSQGTRNK4", "@id": "/biosamples/4DNBSQGTRNK4/", "biosample_category": ["Primary Cells"], "uuid": "9f29af4d-fde9-426e-aa35-b6aa520e677e", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSQGTRNK4", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:27.251775+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961759", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961759"}]}, {"dbxrefs": ["SRA:SRX2961760"], "status": "released", "@id": "/experiments-hi-c/4DNEX4WH19KC/", "files": [{"file_size": 1128632183, "@type": ["FileFastq", "File", "Item"], "upload_key": "5d30d86d-e107-410a-96c3-f92fa31748d4/4DNFI8U9G8BZ.fastq.gz", "@id": "/files-fastq/4DNFI8U9G8BZ/", "md5sum": "c4941649d6261c44e9d929fd946f60fb", "uuid": "5d30d86d-e107-410a-96c3-f92fa31748d4", "paired_end": "1", "file_type": "reads", "display_title": "4DNFI8U9G8BZ.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5d30d86d-e107-410a-96c3-f92fa31748d4/4DNFI8U9G8BZ.fastq.gz", "accession": "4DNFI8U9G8BZ", "href": "/files-fastq/4DNFI8U9G8BZ/@@download/4DNFI8U9G8BZ.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI7W2MXI7/", "paired_end": "2", "uuid": "26341034-7b29-48ed-98ea-4fd9866e1f58", "display_title": "4DNFI7W2MXI7.fastq.gz", "accession": "4DNFI7W2MXI7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/a099221b-7b51-4c2b-b608-2ba5c2157bd8/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "a099221b-7b51-4c2b-b608-2ba5c2157bd8", "Total Sequences": 15589476, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI8U9G8BZ/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 8, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1167497573, "@type": ["FileFastq", "File", "Item"], "upload_key": "26341034-7b29-48ed-98ea-4fd9866e1f58/4DNFI7W2MXI7.fastq.gz", "@id": "/files-fastq/4DNFI7W2MXI7/", "md5sum": "104fc33a28b81abcc09cf51ebf1c77f6", "uuid": "26341034-7b29-48ed-98ea-4fd9866e1f58", "paired_end": "2", "file_type": "reads", "display_title": "4DNFI7W2MXI7.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/26341034-7b29-48ed-98ea-4fd9866e1f58/4DNFI7W2MXI7.fastq.gz", "accession": "4DNFI7W2MXI7", "href": "/files-fastq/4DNFI7W2MXI7/@@download/4DNFI7W2MXI7.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI8U9G8BZ/", "paired_end": "1", "uuid": "5d30d86d-e107-410a-96c3-f92fa31748d4", "display_title": "4DNFI8U9G8BZ.fastq.gz", "accession": "4DNFI8U9G8BZ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/acbe48bb-a9d6-4bf6-a3fc-7cfecd655acf/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "acbe48bb-a9d6-4bf6-a3fc-7cfecd655acf", "Total Sequences": 15589476, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI7W2MXI7/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 8, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "249e8d6b-8312-45b2-82af-b40ed1c24399", "accession": "4DNEX4WH19KC", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEX4WH19KC", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBS8MWUS2W", "@id": "/biosamples/4DNBS8MWUS2W/", "biosample_category": ["Primary Cells"], "uuid": "7728a640-181d-483f-83d8-06fee9078509", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBS8MWUS2W", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:55.181464+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961760", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961760"}]}, {"dbxrefs": ["SRA:SRX2961764"], "status": "released", "@id": "/experiments-hi-c/4DNEXS6OQK33/", "files": [{"file_size": 1322979603, "@type": ["FileFastq", "File", "Item"], "upload_key": "a0a1b036-359c-4673-8100-49436aa38f65/4DNFICBJC1U6.fastq.gz", "@id": "/files-fastq/4DNFICBJC1U6/", "md5sum": "90a9872417a55e6e18343c8c82188da4", "uuid": "a0a1b036-359c-4673-8100-49436aa38f65", "paired_end": "1", "file_type": "reads", "display_title": "4DNFICBJC1U6.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a0a1b036-359c-4673-8100-49436aa38f65/4DNFICBJC1U6.fastq.gz", "accession": "4DNFICBJC1U6", "href": "/files-fastq/4DNFICBJC1U6/@@download/4DNFICBJC1U6.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIJYBF4TH/", "paired_end": "2", "uuid": "8481c1c9-57de-49ce-b08e-a3083d53664c", "display_title": "4DNFIJYBF4TH.fastq.gz", "accession": "4DNFIJYBF4TH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/d843c050-ec53-4b30-bb54-480ae6fa11a6/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "d843c050-ec53-4b30-bb54-480ae6fa11a6", "Total Sequences": 18824811, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICBJC1U6/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 9, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1361499978, "@type": ["FileFastq", "File", "Item"], "upload_key": "8481c1c9-57de-49ce-b08e-a3083d53664c/4DNFIJYBF4TH.fastq.gz", "@id": "/files-fastq/4DNFIJYBF4TH/", "md5sum": "6c50629f8937a2babb146b940241ceea", "uuid": "8481c1c9-57de-49ce-b08e-a3083d53664c", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIJYBF4TH.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/8481c1c9-57de-49ce-b08e-a3083d53664c/4DNFIJYBF4TH.fastq.gz", "accession": "4DNFIJYBF4TH", "href": "/files-fastq/4DNFIJYBF4TH/@@download/4DNFIJYBF4TH.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFICBJC1U6/", "paired_end": "1", "uuid": "a0a1b036-359c-4673-8100-49436aa38f65", "display_title": "4DNFICBJC1U6.fastq.gz", "accession": "4DNFICBJC1U6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/e5f32499-bc3e-4294-9bb2-00e8c2206219/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "e5f32499-bc3e-4294-9bb2-00e8c2206219", "Total Sequences": 18824811, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJYBF4TH/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 9, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "3bb694b4-72cf-49fe-85d1-6fcbf07175ea", "accession": "4DNEXS6OQK33", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXS6OQK33", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBS9BSWPHO", "@id": "/biosamples/4DNBS9BSWPHO/", "biosample_category": ["Primary Cells"], "uuid": "dbb3006f-42f2-4b09-a84f-eb35cce1ec7c", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBS9BSWPHO", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:20.695118+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961764", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961764"}]}, {"dbxrefs": ["SRA:SRX2961766"], "status": "released", "@id": "/experiments-hi-c/4DNEXKBWQZWV/", "files": [{"file_size": 1370768037, "@type": ["FileFastq", "File", "Item"], "upload_key": "2a97618a-4e9b-42d7-9c80-8e72d6eaa22c/4DNFIU57129A.fastq.gz", "@id": "/files-fastq/4DNFIU57129A/", "md5sum": "e1e76103c3c1ad934ff3255772c49009", "uuid": "2a97618a-4e9b-42d7-9c80-8e72d6eaa22c", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIU57129A.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2a97618a-4e9b-42d7-9c80-8e72d6eaa22c/4DNFIU57129A.fastq.gz", "accession": "4DNFIU57129A", "href": "/files-fastq/4DNFIU57129A/@@download/4DNFIU57129A.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFID9OZN15/", "paired_end": "2", "uuid": "37508678-466a-47a9-9bfd-3e18907c11b1", "display_title": "4DNFID9OZN15.fastq.gz", "accession": "4DNFID9OZN15", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/c8637694-ff3d-4d82-87fc-9c5febce0b27/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "c8637694-ff3d-4d82-87fc-9c5febce0b27", "Total Sequences": 19425060, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIU57129A/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 10, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1388131774, "@type": ["FileFastq", "File", "Item"], "upload_key": "37508678-466a-47a9-9bfd-3e18907c11b1/4DNFID9OZN15.fastq.gz", "@id": "/files-fastq/4DNFID9OZN15/", "md5sum": "9193ba32b4b45834ff2f72dbabd989b6", "uuid": "37508678-466a-47a9-9bfd-3e18907c11b1", "paired_end": "2", "file_type": "reads", "display_title": "4DNFID9OZN15.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/37508678-466a-47a9-9bfd-3e18907c11b1/4DNFID9OZN15.fastq.gz", "accession": "4DNFID9OZN15", "href": "/files-fastq/4DNFID9OZN15/@@download/4DNFID9OZN15.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIU57129A/", "paired_end": "1", "uuid": "2a97618a-4e9b-42d7-9c80-8e72d6eaa22c", "display_title": "4DNFIU57129A.fastq.gz", "accession": "4DNFIU57129A", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/659dba54-5bfe-4547-8dd8-7cbadcdc8096/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "659dba54-5bfe-4547-8dd8-7cbadcdc8096", "Total Sequences": 19425060, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFID9OZN15/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 10, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "59066e6a-2150-4386-9377-d2ed329ce457", "accession": "4DNEXKBWQZWV", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXKBWQZWV", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBS2GQXJ1P", "@id": "/biosamples/4DNBS2GQXJ1P/", "biosample_category": ["Primary Cells"], "uuid": "a67231fb-9f6d-4666-a58e-943097850818", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBS2GQXJ1P", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:15.280924+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961766", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961766"}]}, {"dbxrefs": ["SRA:SRX2961767"], "status": "released", "@id": "/experiments-hi-c/4DNEXTQ2S37G/", "files": [{"file_size": 1076181396, "@type": ["FileFastq", "File", "Item"], "upload_key": "678cc6c7-1057-462e-9f04-2b0235a6b62e/4DNFIUGZU6UI.fastq.gz", "@id": "/files-fastq/4DNFIUGZU6UI/", "md5sum": "1b81910670413f24a112ef6bd295b6c0", "uuid": "678cc6c7-1057-462e-9f04-2b0235a6b62e", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIUGZU6UI.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/678cc6c7-1057-462e-9f04-2b0235a6b62e/4DNFIUGZU6UI.fastq.gz", "accession": "4DNFIUGZU6UI", "href": "/files-fastq/4DNFIUGZU6UI/@@download/4DNFIUGZU6UI.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIOFMDSC8/", "paired_end": "2", "uuid": "f2bfc236-6a45-4a9b-ac8d-c82c4e772865", "display_title": "4DNFIOFMDSC8.fastq.gz", "accession": "4DNFIOFMDSC8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/3264a38c-628c-491b-9442-92c505047065/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "3264a38c-628c-491b-9442-92c505047065", "Total Sequences": 15217394, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUGZU6UI/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 11, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1113407923, "@type": ["FileFastq", "File", "Item"], "upload_key": "f2bfc236-6a45-4a9b-ac8d-c82c4e772865/4DNFIOFMDSC8.fastq.gz", "@id": "/files-fastq/4DNFIOFMDSC8/", "md5sum": "086e6e9eea157ff1ac1dbbdfaa1d5ba1", "uuid": "f2bfc236-6a45-4a9b-ac8d-c82c4e772865", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIOFMDSC8.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/f2bfc236-6a45-4a9b-ac8d-c82c4e772865/4DNFIOFMDSC8.fastq.gz", "accession": "4DNFIOFMDSC8", "href": "/files-fastq/4DNFIOFMDSC8/@@download/4DNFIOFMDSC8.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIUGZU6UI/", "paired_end": "1", "uuid": "678cc6c7-1057-462e-9f04-2b0235a6b62e", "display_title": "4DNFIUGZU6UI.fastq.gz", "accession": "4DNFIUGZU6UI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/82c2bfd9-521a-4553-bc77-c450610a0a0c/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "82c2bfd9-521a-4553-bc77-c450610a0a0c", "Total Sequences": 15217394, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOFMDSC8/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 11, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "c95fd0ca-b176-49e7-9a83-04136815e9b9", "accession": "4DNEXTQ2S37G", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXTQ2S37G", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSNIT56NG", "@id": "/biosamples/4DNBSNIT56NG/", "biosample_category": ["Primary Cells"], "uuid": "fd1b7925-b9f8-47d1-9a21-4de1bada34b7", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSNIT56NG", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:40.863079+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961767", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961767"}]}, {"dbxrefs": ["SRA:SRX2961769"], "status": "released", "@id": "/experiments-hi-c/4DNEXJG7S766/", "files": [{"file_size": 1820087396, "@type": ["FileFastq", "File", "Item"], "upload_key": "9449a32c-eaca-4bf2-9f7c-0c281803cbc2/4DNFIMZV1E2H.fastq.gz", "@id": "/files-fastq/4DNFIMZV1E2H/", "md5sum": "82d1f66f7844ee4431fe141238c907be", "uuid": "9449a32c-eaca-4bf2-9f7c-0c281803cbc2", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIMZV1E2H.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9449a32c-eaca-4bf2-9f7c-0c281803cbc2/4DNFIMZV1E2H.fastq.gz", "accession": "4DNFIMZV1E2H", "href": "/files-fastq/4DNFIMZV1E2H/@@download/4DNFIMZV1E2H.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIBQUJ6VC/", "paired_end": "2", "uuid": "182fa952-16f2-4292-9bf7-38b71f5f6098", "display_title": "4DNFIBQUJ6VC.fastq.gz", "accession": "4DNFIBQUJ6VC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/f76ec8d1-223c-4287-9505-89c5ce216b2d/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "f76ec8d1-223c-4287-9505-89c5ce216b2d", "Total Sequences": 25504604, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMZV1E2H/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 12, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1872159047, "@type": ["FileFastq", "File", "Item"], "upload_key": "182fa952-16f2-4292-9bf7-38b71f5f6098/4DNFIBQUJ6VC.fastq.gz", "@id": "/files-fastq/4DNFIBQUJ6VC/", "md5sum": "7f88d3a0e3c32f1ecd0ef4b64c7a960b", "uuid": "182fa952-16f2-4292-9bf7-38b71f5f6098", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIBQUJ6VC.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/182fa952-16f2-4292-9bf7-38b71f5f6098/4DNFIBQUJ6VC.fastq.gz", "accession": "4DNFIBQUJ6VC", "href": "/files-fastq/4DNFIBQUJ6VC/@@download/4DNFIBQUJ6VC.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIMZV1E2H/", "paired_end": "1", "uuid": "9449a32c-eaca-4bf2-9f7c-0c281803cbc2", "display_title": "4DNFIMZV1E2H.fastq.gz", "accession": "4DNFIMZV1E2H", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/a4881d9c-0aa4-44df-b056-8f57670d4b0f/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "a4881d9c-0aa4-44df-b056-8f57670d4b0f", "Total Sequences": 25504604, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBQUJ6VC/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 12, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "f81285c6-c56d-43b9-baa8-8826c329bd9a", "accession": "4DNEXJG7S766", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXJG7S766", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSTUKZPYF", "@id": "/biosamples/4DNBSTUKZPYF/", "biosample_category": ["Primary Cells"], "uuid": "59580995-7d20-437a-bd11-a0dc0e52fc5a", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSTUKZPYF", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:32:25.901619+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX2961769", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX2961769"}]}, {"dbxrefs": ["SRA:SRX3347126"], "status": "released", "@id": "/experiments-hi-c/4DNEXZIJQ1QD/", "files": [{"file_size": 1305311183, "@type": ["FileFastq", "File", "Item"], "upload_key": "141e51a0-ce2c-4e26-b5b0-35e820adc637/4DNFIQZ65RO8.fastq.gz", "@id": "/files-fastq/4DNFIQZ65RO8/", "md5sum": "9bca04dff7596b6000685575511678b7", "uuid": "141e51a0-ce2c-4e26-b5b0-35e820adc637", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIQZ65RO8.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/141e51a0-ce2c-4e26-b5b0-35e820adc637/4DNFIQZ65RO8.fastq.gz", "accession": "4DNFIQZ65RO8", "href": "/files-fastq/4DNFIQZ65RO8/@@download/4DNFIQZ65RO8.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIQJ9LDM8/", "paired_end": "2", "uuid": "a8b28054-1b05-4af1-a52a-19734eae61b8", "display_title": "4DNFIQJ9LDM8.fastq.gz", "accession": "4DNFIQJ9LDM8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/66f75966-e9a5-4e1f-9e48-c30c9aad79cf/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "66f75966-e9a5-4e1f-9e48-c30c9aad79cf", "Total Sequences": 19746819, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQZ65RO8/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 13, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1337324108, "@type": ["FileFastq", "File", "Item"], "upload_key": "a8b28054-1b05-4af1-a52a-19734eae61b8/4DNFIQJ9LDM8.fastq.gz", "@id": "/files-fastq/4DNFIQJ9LDM8/", "md5sum": "bd9fdbd4771570ca6667aeaea1748116", "uuid": "a8b28054-1b05-4af1-a52a-19734eae61b8", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIQJ9LDM8.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a8b28054-1b05-4af1-a52a-19734eae61b8/4DNFIQJ9LDM8.fastq.gz", "accession": "4DNFIQJ9LDM8", "href": "/files-fastq/4DNFIQJ9LDM8/@@download/4DNFIQJ9LDM8.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIQZ65RO8/", "paired_end": "1", "uuid": "141e51a0-ce2c-4e26-b5b0-35e820adc637", "display_title": "4DNFIQZ65RO8.fastq.gz", "accession": "4DNFIQZ65RO8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/cb56555e-7ea0-4808-97e9-2ec7d27f6db9/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "cb56555e-7ea0-4808-97e9-2ec7d27f6db9", "Total Sequences": 19746819, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQJ9LDM8/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 13, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "ac067405-296a-4842-ba3c-7ce0d604057e", "accession": "4DNEXZIJQ1QD", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXZIJQ1QD", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSB5HWUDG", "@id": "/biosamples/4DNBSB5HWUDG/", "biosample_category": ["Primary Cells"], "uuid": "685dba99-7236-48d7-bd98-84eaca932589", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSB5HWUDG", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:45.431691+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX3347126", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX3347126"}]}, {"dbxrefs": ["SRA:SRX3347127"], "status": "released", "@id": "/experiments-hi-c/4DNEXB8X9LR4/", "files": [{"file_size": 1197192724, "@type": ["FileFastq", "File", "Item"], "upload_key": "9c1a4e77-2c8b-4b73-86d3-1d10b4627fa2/4DNFITM65RAF.fastq.gz", "@id": "/files-fastq/4DNFITM65RAF/", "md5sum": "bcfc33e983e6783966455fbd70a12e43", "uuid": "9c1a4e77-2c8b-4b73-86d3-1d10b4627fa2", "paired_end": "1", "file_type": "reads", "display_title": "4DNFITM65RAF.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9c1a4e77-2c8b-4b73-86d3-1d10b4627fa2/4DNFITM65RAF.fastq.gz", "accession": "4DNFITM65RAF", "href": "/files-fastq/4DNFITM65RAF/@@download/4DNFITM65RAF.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIGWBQW9T/", "paired_end": "2", "uuid": "2c1c9f60-abfd-43eb-bf04-10f4be8286cd", "display_title": "4DNFIGWBQW9T.fastq.gz", "accession": "4DNFIGWBQW9T", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/98699c02-04e3-4ba5-bc44-d05d59e06d53/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "98699c02-04e3-4ba5-bc44-d05d59e06d53", "Total Sequences": 18144466, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITM65RAF/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 14, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1228432928, "@type": ["FileFastq", "File", "Item"], "upload_key": "2c1c9f60-abfd-43eb-bf04-10f4be8286cd/4DNFIGWBQW9T.fastq.gz", "@id": "/files-fastq/4DNFIGWBQW9T/", "md5sum": "22ba9b403b8913d6bebe0b1ecdbe2b65", "uuid": "2c1c9f60-abfd-43eb-bf04-10f4be8286cd", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIGWBQW9T.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2c1c9f60-abfd-43eb-bf04-10f4be8286cd/4DNFIGWBQW9T.fastq.gz", "accession": "4DNFIGWBQW9T", "href": "/files-fastq/4DNFIGWBQW9T/@@download/4DNFIGWBQW9T.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFITM65RAF/", "paired_end": "1", "uuid": "9c1a4e77-2c8b-4b73-86d3-1d10b4627fa2", "display_title": "4DNFITM65RAF.fastq.gz", "accession": "4DNFITM65RAF", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/b4a310f7-3001-4813-ba2d-265bb83bb65f/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "b4a310f7-3001-4813-ba2d-265bb83bb65f", "Total Sequences": 18144466, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGWBQW9T/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 14, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "1cd4dffc-a650-43a0-b244-b81ee6ad5ae6", "accession": "4DNEXB8X9LR4", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXB8X9LR4", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSZ6RQV57", "@id": "/biosamples/4DNBSZ6RQV57/", "biosample_category": ["Primary Cells"], "uuid": "d6f1ccc2-8c56-4f44-9645-7f042d4f4d1d", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSZ6RQV57", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:25.520003+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX3347127", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX3347127"}]}, {"dbxrefs": ["SRA:SRX3347128"], "status": "released", "@id": "/experiments-hi-c/4DNEXYD9WRE2/", "files": [{"file_size": 1192988567, "@type": ["FileFastq", "File", "Item"], "upload_key": "a1939fb8-cb34-43ca-a7ef-4ce1bab71660/4DNFI4NF8RH9.fastq.gz", "@id": "/files-fastq/4DNFI4NF8RH9/", "md5sum": "69abaed885616bdf6524579687307b53", "uuid": "a1939fb8-cb34-43ca-a7ef-4ce1bab71660", "paired_end": "1", "file_type": "reads", "display_title": "4DNFI4NF8RH9.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a1939fb8-cb34-43ca-a7ef-4ce1bab71660/4DNFI4NF8RH9.fastq.gz", "accession": "4DNFI4NF8RH9", "href": "/files-fastq/4DNFI4NF8RH9/@@download/4DNFI4NF8RH9.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIOKN9Q5S/", "paired_end": "2", "uuid": "1ab929ef-94c3-4a91-8c46-01919b8ef9b7", "display_title": "4DNFIOKN9Q5S.fastq.gz", "accession": "4DNFIOKN9Q5S", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/b3503516-0677-4368-b443-160cee1b778e/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "b3503516-0677-4368-b443-160cee1b778e", "Total Sequences": 18789602, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4NF8RH9/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 15, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 1228877521, "@type": ["FileFastq", "File", "Item"], "upload_key": "1ab929ef-94c3-4a91-8c46-01919b8ef9b7/4DNFIOKN9Q5S.fastq.gz", "@id": "/files-fastq/4DNFIOKN9Q5S/", "md5sum": "43b481444e819fbe430f614d73dde7a0", "uuid": "1ab929ef-94c3-4a91-8c46-01919b8ef9b7", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIOKN9Q5S.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/1ab929ef-94c3-4a91-8c46-01919b8ef9b7/4DNFIOKN9Q5S.fastq.gz", "accession": "4DNFIOKN9Q5S", "href": "/files-fastq/4DNFIOKN9Q5S/@@download/4DNFIOKN9Q5S.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI4NF8RH9/", "paired_end": "1", "uuid": "a1939fb8-cb34-43ca-a7ef-4ce1bab71660", "display_title": "4DNFI4NF8RH9.fastq.gz", "accession": "4DNFI4NF8RH9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/2fa032f0-8618-4183-b706-00af3b27382a/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "2fa032f0-8618-4183-b706-00af3b27382a", "Total Sequences": 18789602, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOKN9Q5S/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 15, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "1b9b4101-5e76-4d74-976b-928c94aa1487", "accession": "4DNEXYD9WRE2", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEXYD9WRE2", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSGU4G89X", "@id": "/biosamples/4DNBSGU4G89X/", "biosample_category": ["Primary Cells"], "uuid": "3c476747-be1f-4c9b-b344-9ff58b55e504", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSGU4G89X", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:26.600283+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX3347128", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX3347128"}]}, {"dbxrefs": ["SRA:SRX3347143"], "status": "released", "@id": "/experiments-hi-c/4DNEX1YNIZLY/", "files": [{"file_size": 878692743, "@type": ["FileFastq", "File", "Item"], "upload_key": "3e142bec-f464-4bbb-8115-2bbec15ee359/4DNFIMC8C8QU.fastq.gz", "@id": "/files-fastq/4DNFIMC8C8QU/", "md5sum": "242b33540b5deb18cb0bfe08c185bba5", "uuid": "3e142bec-f464-4bbb-8115-2bbec15ee359", "paired_end": "1", "file_type": "reads", "display_title": "4DNFIMC8C8QU.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/3e142bec-f464-4bbb-8115-2bbec15ee359/4DNFIMC8C8QU.fastq.gz", "accession": "4DNFIMC8C8QU", "href": "/files-fastq/4DNFIMC8C8QU/@@download/4DNFIMC8C8QU.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIJGINVEZ/", "paired_end": "2", "uuid": "564662f0-dc29-46ab-837a-cdbeb7139ee1", "display_title": "4DNFIJGINVEZ.fastq.gz", "accession": "4DNFIJGINVEZ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/4abb0828-d7ec-4588-a056-5eb440eb43f7/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "4abb0828-d7ec-4588-a056-5eb440eb43f7", "Total Sequences": 12905075, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMC8C8QU/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 16, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 908931134, "@type": ["FileFastq", "File", "Item"], "upload_key": "564662f0-dc29-46ab-837a-cdbeb7139ee1/4DNFIJGINVEZ.fastq.gz", "@id": "/files-fastq/4DNFIJGINVEZ/", "md5sum": "216a24b83f49ddba8212fa4de4aa16e5", "uuid": "564662f0-dc29-46ab-837a-cdbeb7139ee1", "paired_end": "2", "file_type": "reads", "display_title": "4DNFIJGINVEZ.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/564662f0-dc29-46ab-837a-cdbeb7139ee1/4DNFIJGINVEZ.fastq.gz", "accession": "4DNFIJGINVEZ", "href": "/files-fastq/4DNFIJGINVEZ/@@download/4DNFIJGINVEZ.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIMC8C8QU/", "paired_end": "1", "uuid": "3e142bec-f464-4bbb-8115-2bbec15ee359", "display_title": "4DNFIMC8C8QU.fastq.gz", "accession": "4DNFIMC8C8QU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/7488975a-4c08-41f4-a6d8-19ed388b65e2/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "7488975a-4c08-41f4-a6d8-19ed388b65e2", "Total Sequences": 12905075, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJGINVEZ/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 16, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "d0450986-0142-4f3a-8b35-be636509c8f2", "accession": "4DNEX1YNIZLY", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEX1YNIZLY", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBS24RLB7F", "@id": "/biosamples/4DNBS24RLB7F/", "biosample_category": ["Primary Cells"], "uuid": "951aff23-9180-416f-a59d-3c2fe333297d", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBS24RLB7F", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:37.526849+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX3347143", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX3347143"}]}, {"dbxrefs": ["SRA:SRX3347144"], "status": "released", "@id": "/experiments-hi-c/4DNEX55MBKJJ/", "files": [{"file_size": 899771874, "@type": ["FileFastq", "File", "Item"], "upload_key": "e9da5297-3fbd-4d8e-ad3b-92108278e70f/4DNFI4ASINGR.fastq.gz", "@id": "/files-fastq/4DNFI4ASINGR/", "md5sum": "4cec8a01f3415ce29ff4b390e85f0603", "uuid": "e9da5297-3fbd-4d8e-ad3b-92108278e70f", "paired_end": "1", "file_type": "reads", "display_title": "4DNFI4ASINGR.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e9da5297-3fbd-4d8e-ad3b-92108278e70f/4DNFI4ASINGR.fastq.gz", "accession": "4DNFI4ASINGR", "href": "/files-fastq/4DNFI4ASINGR/@@download/4DNFI4ASINGR.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFILY7P1PM/", "paired_end": "2", "uuid": "5009a230-321d-4fd4-88ea-e95e72e2211c", "display_title": "4DNFILY7P1PM.fastq.gz", "accession": "4DNFILY7P1PM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/10341a67-da3b-469e-aaea-fff74e268e64/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "10341a67-da3b-469e-aaea-fff74e268e64", "Total Sequences": 13148033, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI4ASINGR/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 17, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_size": 927278343, "@type": ["FileFastq", "File", "Item"], "upload_key": "5009a230-321d-4fd4-88ea-e95e72e2211c/4DNFILY7P1PM.fastq.gz", "@id": "/files-fastq/4DNFILY7P1PM/", "md5sum": "6497159acbd9a2b7795f05005885b92c", "uuid": "5009a230-321d-4fd4-88ea-e95e72e2211c", "paired_end": "2", "file_type": "reads", "display_title": "4DNFILY7P1PM.fastq.gz", "file_classification": "raw file", "status": "released", "file_type_detailed": "reads (fastq)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5009a230-321d-4fd4-88ea-e95e72e2211c/4DNFILY7P1PM.fastq.gz", "accession": "4DNFILY7P1PM", "href": "/files-fastq/4DNFILY7P1PM/@@download/4DNFILY7P1PM.fastq.gz", "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "status": "released", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFI4ASINGR/", "paired_end": "1", "uuid": "e9da5297-3fbd-4d8e-ad3b-92108278e70f", "display_title": "4DNFI4ASINGR.fastq.gz", "accession": "4DNFI4ASINGR", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "@id": "/file-formats/fastq/", "file_format": "fastq", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/85bd97bd-96d7-4439-9156-0ec2a521b6ad/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "85bd97bd-96d7-4439-9156-0ec2a521b6ad", "Total Sequences": 13148033, "status": "released", "display_title": "QualityMetricFastqc from 2018-07-03", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFILY7P1PM/fastqc_report.html", "Sequence length": "125", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "contributing_labs": [{"name": "leonid-mirny-lab", "status": "current", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}], "lab": {"name": "kikue-tachibana-lab", "@id": "/labs/kikue-tachibana-lab/", "uuid": "55972313-cb04-43ad-835b-c83dac4eec9e", "display_title": "Kikue Tachibana, IMBA", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.55972313-cb04-43ad-835b-c83dac4eec9e"]}}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Kikue Tachibana, IMBA", "experiment_type": "sn-Hi-C", "experiment_bucket": "raw file", "assay_info": "DpnII", "replicate_info": "Biorep 17, Techrep 1", "biosource_name": "animal zygote", "lab_name": "Kikue Tachibana, IMBA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "500c6289-4d10-42f3-9363-4b82f7ee94eb", "accession": "4DNEX55MBKJJ", "display_title": "sn-Hi-C on animal zygote with DpnII - 4DNEX55MBKJJ", "biosample": {"biosource_summary": "animal zygote", "accession": "4DNBSL3PD969", "@id": "/biosamples/4DNBSL3PD969/", "biosample_category": ["Primary Cells"], "uuid": "6029978e-6fa0-486e-90f7-5aca4b0ecb0d", "treatments_summary": "None", "@type": ["Biosample", "Item"], "display_title": "4DNBSL3PD969", "modifications_summary": "None", "status": "released", "biosample_type": "primary cells", "modifications": [], "treatments": [], "biosource": [{"display_title": "animal zygote - 4DNSRE9KV1IZ", "biosource_type": "primary cell", "@id": "/biosources/4DNSRE9KV1IZ/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "accession": "4DNSRE9KV1IZ", "uuid": "3add03b3-8bf9-4ae1-b447-147560618559", "status": "released", "cell_line": {"term_name": "animal zygote", "preferred_name": "animal zygote", "display_title": "animal zygote", "synonyms": ["Zygote:1-cell"], "uuid": "083776ff-12aa-4a1e-bddd-bbd2a2c96362", "@type": ["OntologyTerm", "Item"], "status": "released", "@id": "/ontology-terms/CL:0000365/", "term_id": "CL:0000365", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "name": "mouse", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/sn-hi-c/", "display_title": "sn-Hi-C", "assay_classification": "3C via Ligation", "uuid": "7a0f628b-cf79-4ac9-8f03-77a1f9c73ed7", "assay_subclass_short": "Hi-C (single cell)", "@type": ["ExperimentType", "Item"], "status": "released", "other_tags": ["DNA-DNA", "Single Cell", "3D", "Pairwise"], "experiment_category": "Sequencing", "title": "sn-Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions - Single Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"@type": ["Enzyme", "Item"], "status": "released", "name": "DpnII", "display_title": "DpnII", "@id": "/enzymes/DpnII/", "uuid": "356a57a1-1f1d-463d-a972-27742f79a6a5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-05-20T22:33:16.808664+00:00"}, "experiment_categorizer": {"combined": "Enzyme: DpnII", "field": "Enzyme", "value": "DpnII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": [{"ref": "SRA:SRX3347144", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX3347144"}]}], "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESTRAR8I6/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "c4d84d81-f92e-4fbb-a0d4-c0e42df61424", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESTRAR8I6", "external_references": [{"ref": "GEO:GSE100569", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100569"}], "produced_in_pub": {"journal": "The EMBO journal", "authors": ["Gassler J", "Brandao HB", "Imakaev M", "Flyamer IM", "Ladstatter S", "Bickmore WA", "Peters JM", "Mirny LA", "Tachibana K"], "date_published": "2017-12-07", "title": "A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.", "url": "https://www.ncbi.nlm.nih.gov/pubmed/29217590", "short_attribution": "Gassler J et al. (2017)", "status": "current", "uuid": "856a6952-ecc0-4bbf-9e6d-77d07652624f", "@id": "/publications/856a6952-ecc0-4bbf-9e6d-77d07652624f/", "@type": ["Publication", "Item"], "display_title": "Gassler J et al. (2017) PMID:29217590", "abstract": "Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naive paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic  chromatin conformations are assembled. Here, we investigated whether a mechanism  of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically  depend on Scc1-cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi-C, suggesting a mechanism where cohesin locally compacts chromatin by active loop extrusion, whose processivity is controlled by Wapl. Our simulations  and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onward.", "ID": "PMID:29217590", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"@id": "/publications/856a6952-ecc0-4bbf-9e6d-77d07652624f/", "journal": "The EMBO journal", "abstract": "Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naive paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic  chromatin conformations are assembled. Here, we investigated whether a mechanism  of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically  depend on Scc1-cohesin and that are regulated in size and linear density by Wapl. Remarkably, we discovered distinct effects on maternal and paternal chromatin loop sizes, likely reflecting differences in loop extrusion dynamics and epigenetic reprogramming. Dynamic polymer models of chromosomes reproduce changes in snHi-C, suggesting a mechanism where cohesin locally compacts chromatin by active loop extrusion, whose processivity is controlled by Wapl. Our simulations  and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onward.", "@type": ["Publication", "Item"], "title": "A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.", "status": "current", "date_published": "2017-12-07", "authors": ["Gassler J", "Brandao HB", "Imakaev M", "Flyamer IM", "Ladstatter S", "Bickmore WA", "Peters JM", "Mirny LA", "Tachibana K"], "uuid": "856a6952-ecc0-4bbf-9e6d-77d07652624f", "ID": "PMID:29217590", "display_title": "Gassler J et al. (2017) PMID:29217590", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 17, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}