{"lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "title": "Yijun Ruan, JAX", "status": "current", "correspondence": [{"contact_email": "eWlqdW4ucnVhbkBqYXgub3Jn", "@id": "/users/d8ac229e-ec08-4411-be38-dc779520ea62/", "display_title": "Yijun Ruan"}], "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "award": {"uuid": "029a2578-43dc-4343-8f41-694518cce304", "@type": ["Award", "Item"], "status": "current", "project": "4DN", "description": "NOFIC: This proposal seeks to fulfill a community need for a comprehensive, high-resolution genome-mapping platform that will enable investigation of the structural, functional and spatiotemporal organization of the human genome. Our ultimate goal is to deliver complex chromatin interaction network maps in the context of 3D genome structures from which the dynamics of individual genomic elements can be monitored and referenced. Here, we propose to develop a Nucleome Positioning System (NPS)-comprised of 1) a robust genome- wide mapping technology platform, 2) advanced computational modeling algorithms and 3) state-of-the-art nuclear imaging methods-that will allow users community-wide to uncover the regulatory functions of 3D genome organization in human cells. NPS will be based upon the established ChIA-PET method (1,2), enhanced by process optimizations-i.e., microfluidic-based miniaturization and Tn5-transposase-based library preparation-to facilitate the study of chromatin interactions mediated by protein factors across a broader range of human cell types (Aim 1, see also Mapping Technology Development Component). We will also optimize RICh-PET for the comprehensive mapping of chromatin interactions mediated by non-coding RNAs (Aim 1). The high-quality mapping data generated through these optimization efforts will be analyzed by a new computational platform (Three-Dimensional Nucleome Modeling Engine, or 3D-NOME) that makes use of hierarchical multi-scaling to model 3D genome structures (Aim 2, Data Analysis and Modeling component). We will also complement the 3D modeling with transcriptome, epigenome and SNP data associated with genetic diseases (GWAS) to provide functional annotation to structural units (Aim 2). We will continue by developing strategies to validate the nucleome geometry predicted by 3D-NOME both structurally, using new nuclear imaging technologies, and functionally, using cutting-edge genome- and epigenome-editing approaches, in both human cell lines and mouse models (Aim 3, Biological Validation Component). Finally, we will implement NPS to generate pilot 3D genome maps from a wide range of human cell lines and primary immune cells sorted from whole blood, to elucidate the spatiotemporal dynamics of human genome organization over major developmental and hematopoietic cell lineages, as well as among differentiating lymphocytes involved in the immune response (Aim 4, Data Generation Component). Together, these efforts will yield a powerful set of sophisticated, high-quality tools and mapping data for the larger research community, and will help establish the standards for future 3D/4D nucleome studies. They will also provide insights into the broad mechanisms that organize the structure and regulate the function of the human genome, as well as the specific mechanisms by which immune responses are regulated at the nuclear level.", "center_title": "NOFIC - Ruan", "name": "1U54DK107967-01", "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "@id": "/awards/1U54DK107967-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["ruan-lab:GM19239-nonenriched-chiadrop"], "accession": "4DNESXGXZEZ6", "description": "Replicates of non-enriched ChIA-Drop on GM19239 cells.", "date_created": "2020-05-22T05:48:00.961800+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Non-enriched ChIA-Drop on GM19239", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-06-16T17:01:14.973140+00:00"}, "public_release": "2020-05-28", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXP949DLF/", "display_title": "ChIA-Drop on GM19239 - 4DNEXP949DLF", "accession": "4DNEXP949DLF", "uuid": "8e945778-4004-4161-8189-aa1e293fc528", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEX634U83C/", "display_title": "ChIA-Drop on GM19239 - 4DNEX634U83C", "accession": "4DNEX634U83C", "uuid": "2858e917-ea21-43a2-a854-f8bae962e04b", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 3, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXZS9Z3LH/", "display_title": "ChIA-Drop on GM19239 - 4DNEXZS9Z3LH", "accession": "4DNEXZS9Z3LH", "uuid": "eab95c02-f23b-4a4d-abb0-35a04bb46776", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 4, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXE8G8594/", "display_title": "ChIA-Drop on GM19239 - 4DNEXE8G8594", "accession": "4DNEXE8G8594", "uuid": "8a26ecef-c571-4e1d-bfb0-1733b08b6649", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 5, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXWUNIGMP/", "display_title": "ChIA-Drop on GM19239 - 4DNEXWUNIGMP", "accession": "4DNEXWUNIGMP", "uuid": "e8d074d0-e784-4e7f-817a-faa3f616ccfe", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 6, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEX3DSSDC5/", "display_title": "ChIA-Drop on GM19239 - 4DNEX3DSSDC5", "accession": "4DNEX3DSSDC5", "uuid": "1dea6c91-df04-4288-bf7e-ec3de4b33dbb", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 7, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXBJ5AYVJ/", "display_title": "ChIA-Drop on GM19239 - 4DNEXBJ5AYVJ", "accession": "4DNEXBJ5AYVJ", "uuid": "fa42b5d7-574b-4fbc-80cc-aac5d8e7a28d", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 8, "tec_rep_no": 1, "replicate_exp": {"@id": "/experiments-seq/4DNEXDWB7B1J/", "display_title": "ChIA-Drop on GM19239 - 4DNEXDWB7B1J", "accession": "4DNEXDWB7B1J", "uuid": "c2370412-d2ad-4387-8649-f246fc930ad1", "@type": ["ExperimentSeq", "Experiment", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "name": "item-page-headers.ExperimentSet.data-usage-guidelines", "award": {"@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Data Usage Guidelines", "status": "released", "aliases": [], "options": {"filetype": "md", "title_icon": "exclamation-circle", "collapsible": false, "default_open": true}, "date_created": "2018-08-06T03:09:55.543206+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-09T09:31:34.537494+00:00"}, "schema_version": "2", "@id": "/static-sections/621e8359-3885-40ce-965d-91894aa7b758/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "621e8359-3885-40ce-965d-91894aa7b758", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267228139"]}, "display_title": "Data Usage Guidelines", "external_references": [], "content": "\n**Data Use Guidelines:** This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) \nand the 4DN Data Portal paper \n([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).", "filetype": "md", "content_as_html": "<div class=\"markdown-container\"><p><strong>Data Use Guidelines:</strong> This is a data set generated by the \n4DN Network and made freely available to the scientific \ncommunity. If you are intending to use these data for a \npublication, we ask that you please contact the data \ngenerating lab to discuss possible coordinated publication. \nIn your manuscript, please cite the 4DN White Paper \n(<a href=\"https://doi.org/10.1038/nature23884\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/nature23884</a>) \nand the 4DN Data Portal paper \n(<a href=\"https://doi.org/10.1038/s41467-022-29697-4\" rel=\"noopener noreferrer\" target=\"_blank\">doi:10.1038/s41467-022-29697-4</a>), \nand please acknowledge the 4DN lab which generated the data. Please direct any questions to the <a href=\"mailto:support@4dnucleome.org\">Data Coordination and Integration Center</a>.</p></div>"}], "project_release": "2020-05-28", "experiments_in_set": [{"@id": "/experiments-seq/4DNEXP949DLF/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "8e945778-4004-4161-8189-aa1e293fc528", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/2757f7e4-96cb-4f76-93bb-b8e2f36d9ca2/4DNFIZBLNUPQ.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "2757f7e4-96cb-4f76-93bb-b8e2f36d9ca2", "display_title": "4DNFIZBLNUPQ.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIZBLNUPQ/", "href": "/files-fastq/4DNFIZBLNUPQ/@@download/4DNFIZBLNUPQ.fastq.gz", "md5sum": "6932c463e51644faf79370ac1dbeeffd", "file_classification": "raw file", "file_size": 29799993811, "upload_key": "2757f7e4-96cb-4f76-93bb-b8e2f36d9ca2/4DNFIZBLNUPQ.fastq.gz", "accession": "4DNFIZBLNUPQ", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "e2128c44-8c22-4e79-9570-0e892c13b7e0", "status": "released", "display_title": "4DNFIAPM2JWK.fastq.gz", "@id": "/files-fastq/4DNFIAPM2JWK/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIAPM2JWK", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZBLNUPQ/fastqc_report.html", "status": "released", "Total Sequences": 399923100, "@id": "/quality-metrics-fastqc/07c0d3c5-36ab-4bbc-8810-9f476f57c7cb/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "07c0d3c5-36ab-4bbc-8810-9f476f57c7cb", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/e2128c44-8c22-4e79-9570-0e892c13b7e0/4DNFIAPM2JWK.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "e2128c44-8c22-4e79-9570-0e892c13b7e0", "display_title": "4DNFIAPM2JWK.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIAPM2JWK/", "href": "/files-fastq/4DNFIAPM2JWK/@@download/4DNFIAPM2JWK.fastq.gz", "md5sum": "ef299e3a50f10e74fd1a335858b9f0df", "file_classification": "raw file", "file_size": 31280493090, "upload_key": "e2128c44-8c22-4e79-9570-0e892c13b7e0/4DNFIAPM2JWK.fastq.gz", "accession": "4DNFIAPM2JWK", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "2757f7e4-96cb-4f76-93bb-b8e2f36d9ca2", "status": "released", "display_title": "4DNFIZBLNUPQ.fastq.gz", "@id": "/files-fastq/4DNFIZBLNUPQ/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIZBLNUPQ", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAPM2JWK/fastqc_report.html", "status": "released", "Total Sequences": 399923100, "@id": "/quality-metrics-fastqc/22282bce-fcda-4643-b9d4-407d6dfd4541/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "22282bce-fcda-4643-b9d4-407d6dfd4541", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXP949DLF", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEXP949DLF", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBS76PQJ1M", "status": "released", "display_title": "4DNBS76PQJ1M", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBS76PQJ1M/", "treatments_summary": "None", "uuid": "bd021e1b-5e7b-4c69-89da-95998cbe488c", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "7402a6f9-129d-4440-bc1f-8d67f2ecac63", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/7402a6f9-129d-4440-bc1f-8d67f2ecac63/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFIC8ZWG5X", "href": "/files-processed/4DNFIC8ZWG5X/@@download/4DNFIC8ZWG5X.txt.gz", "file_size": 29678695, "uuid": "a0a834f2-304f-4bd8-9ae6-1bcfce55c2df", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a0a834f2-304f-4bd8-9ae6-1bcfce55c2df/4DNFIC8ZWG5X.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFIC8ZWG5X/", "md5sum": "6834ebebf7cee91c594363e7bff7da0c", "display_title": "4DNFIC8ZWG5X.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:32.048679+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:15.481228+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEX634U83C/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "2858e917-ea21-43a2-a854-f8bae962e04b", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4d2985f7-d5fb-4115-994e-31683e64f727/4DNFICRADTGZ.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "4d2985f7-d5fb-4115-994e-31683e64f727", "display_title": "4DNFICRADTGZ.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFICRADTGZ/", "href": "/files-fastq/4DNFICRADTGZ/@@download/4DNFICRADTGZ.fastq.gz", "md5sum": "92e4cf5c01bb523c88b7d8b8d37818af", "file_classification": "raw file", "file_size": 32867039064, "upload_key": "4d2985f7-d5fb-4115-994e-31683e64f727/4DNFICRADTGZ.fastq.gz", "accession": "4DNFICRADTGZ", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "bc2eee0c-6e79-4b24-a8e4-c7b0f5ae1d7a", "status": "released", "display_title": "4DNFI73Q7VWO.fastq.gz", "@id": "/files-fastq/4DNFI73Q7VWO/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFI73Q7VWO", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFICRADTGZ/fastqc_report.html", "status": "released", "Total Sequences": 438881415, "@id": "/quality-metrics-fastqc/27ca0b11-3860-4450-a362-438f055f243d/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "27ca0b11-3860-4450-a362-438f055f243d", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/bc2eee0c-6e79-4b24-a8e4-c7b0f5ae1d7a/4DNFI73Q7VWO.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "bc2eee0c-6e79-4b24-a8e4-c7b0f5ae1d7a", "display_title": "4DNFI73Q7VWO.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFI73Q7VWO/", "href": "/files-fastq/4DNFI73Q7VWO/@@download/4DNFI73Q7VWO.fastq.gz", "md5sum": "0fe8b7353019ca9fbb9241df6ec7a34b", "file_classification": "raw file", "file_size": 34291005774, "upload_key": "bc2eee0c-6e79-4b24-a8e4-c7b0f5ae1d7a/4DNFI73Q7VWO.fastq.gz", "accession": "4DNFI73Q7VWO", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "4d2985f7-d5fb-4115-994e-31683e64f727", "status": "released", "display_title": "4DNFICRADTGZ.fastq.gz", "@id": "/files-fastq/4DNFICRADTGZ/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFICRADTGZ", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI73Q7VWO/fastqc_report.html", "status": "released", "Total Sequences": 438881415, "@id": "/quality-metrics-fastqc/5899b1e1-e808-407b-8b03-c03a2703fc7a/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "5899b1e1-e808-407b-8b03-c03a2703fc7a", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEX634U83C", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEX634U83C", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBSDFLXDEE", "status": "released", "display_title": "4DNBSDFLXDEE", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBSDFLXDEE/", "treatments_summary": "None", "uuid": "c7636396-701c-4276-94e9-b793e57e8ac6", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "013a6944-fe9f-4751-acd4-ceb9eb299b37", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/013a6944-fe9f-4751-acd4-ceb9eb299b37/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFI68UGSLZ", "href": "/files-processed/4DNFI68UGSLZ/@@download/4DNFI68UGSLZ.txt.gz", "file_size": 27266086, "uuid": "91a3a377-597c-4337-a05e-0c0ea98ad40f", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/91a3a377-597c-4337-a05e-0c0ea98ad40f/4DNFI68UGSLZ.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFI68UGSLZ/", "md5sum": "45ee52d39b415427c7697e2d23d962b9", "display_title": "4DNFI68UGSLZ.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:31.371430+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:16.109393+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEXZS9Z3LH/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "eab95c02-f23b-4a4d-abb0-35a04bb46776", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a000d93d-9389-4442-a1eb-9b5ec12338dd/4DNFIY8ON7DW.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "a000d93d-9389-4442-a1eb-9b5ec12338dd", "display_title": "4DNFIY8ON7DW.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIY8ON7DW/", "href": "/files-fastq/4DNFIY8ON7DW/@@download/4DNFIY8ON7DW.fastq.gz", "md5sum": "618f3dc515c433b2ff4528cb1f0d65e8", "file_classification": "raw file", "file_size": 31225999790, "upload_key": "a000d93d-9389-4442-a1eb-9b5ec12338dd/4DNFIY8ON7DW.fastq.gz", "accession": "4DNFIY8ON7DW", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "0f9a0233-ea0a-43ac-bb67-9c66d3d96569", "status": "released", "display_title": "4DNFI1LDBQE8.fastq.gz", "@id": "/files-fastq/4DNFI1LDBQE8/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFI1LDBQE8", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIY8ON7DW/fastqc_report.html", "status": "released", "Total Sequences": 417917156, "@id": "/quality-metrics-fastqc/249f5321-ac1c-4ab8-a9b3-6689e4f7025a/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "249f5321-ac1c-4ab8-a9b3-6689e4f7025a", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/0f9a0233-ea0a-43ac-bb67-9c66d3d96569/4DNFI1LDBQE8.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "0f9a0233-ea0a-43ac-bb67-9c66d3d96569", "display_title": "4DNFI1LDBQE8.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFI1LDBQE8/", "href": "/files-fastq/4DNFI1LDBQE8/@@download/4DNFI1LDBQE8.fastq.gz", "md5sum": "9b955f3db425754f87489c8b6426b00c", "file_classification": "raw file", "file_size": 32625510465, "upload_key": "0f9a0233-ea0a-43ac-bb67-9c66d3d96569/4DNFI1LDBQE8.fastq.gz", "accession": "4DNFI1LDBQE8", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "a000d93d-9389-4442-a1eb-9b5ec12338dd", "status": "released", "display_title": "4DNFIY8ON7DW.fastq.gz", "@id": "/files-fastq/4DNFIY8ON7DW/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIY8ON7DW", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1LDBQE8/fastqc_report.html", "status": "released", "Total Sequences": 417917156, "@id": "/quality-metrics-fastqc/41f99733-b4dc-4f51-a9b7-31e7b4f2d5b4/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "41f99733-b4dc-4f51-a9b7-31e7b4f2d5b4", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXZS9Z3LH", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEXZS9Z3LH", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBSW5FE37E", "status": "released", "display_title": "4DNBSW5FE37E", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBSW5FE37E/", "treatments_summary": "None", "uuid": "5cc5f2ae-4d7e-417c-bd78-e9d0604a4191", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "781b26da-876f-4323-a6d3-23206c4a570c", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/781b26da-876f-4323-a6d3-23206c4a570c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFIEYBHDMB", "href": "/files-processed/4DNFIEYBHDMB/@@download/4DNFIEYBHDMB.txt.gz", "file_size": 20696272, "uuid": "b94ce5d2-3a96-4678-86c2-ed4834995819", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b94ce5d2-3a96-4678-86c2-ed4834995819/4DNFIEYBHDMB.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFIEYBHDMB/", "md5sum": "a71d7dc881664c20d2ed57c1db54fd43", "display_title": "4DNFIEYBHDMB.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:30.781828+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:16.880103+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEXE8G8594/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "8a26ecef-c571-4e1d-bfb0-1733b08b6649", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/395852cd-d845-4d0f-978a-955c1e1952c9/4DNFI9TIAPYT.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "395852cd-d845-4d0f-978a-955c1e1952c9", "display_title": "4DNFI9TIAPYT.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFI9TIAPYT/", "href": "/files-fastq/4DNFI9TIAPYT/@@download/4DNFI9TIAPYT.fastq.gz", "md5sum": "2b1688be6628b0cbe7a596a9dda0d9e5", "file_classification": "raw file", "file_size": 30561389306, "upload_key": "395852cd-d845-4d0f-978a-955c1e1952c9/4DNFI9TIAPYT.fastq.gz", "accession": "4DNFI9TIAPYT", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "380b4346-d218-461a-a47d-1892e062f45b", "status": "released", "display_title": "4DNFIUAJM6YE.fastq.gz", "@id": "/files-fastq/4DNFIUAJM6YE/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIUAJM6YE", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9TIAPYT/fastqc_report.html", "status": "released", "Total Sequences": 410284237, "@id": "/quality-metrics-fastqc/a92a7c64-58cb-4d2b-8984-e77287d36d45/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "a92a7c64-58cb-4d2b-8984-e77287d36d45", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/380b4346-d218-461a-a47d-1892e062f45b/4DNFIUAJM6YE.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "380b4346-d218-461a-a47d-1892e062f45b", "display_title": "4DNFIUAJM6YE.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIUAJM6YE/", "href": "/files-fastq/4DNFIUAJM6YE/@@download/4DNFIUAJM6YE.fastq.gz", "md5sum": "05cdc0749c0a88532c8a6ceabccab101", "file_classification": "raw file", "file_size": 31965566480, "upload_key": "380b4346-d218-461a-a47d-1892e062f45b/4DNFIUAJM6YE.fastq.gz", "accession": "4DNFIUAJM6YE", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "395852cd-d845-4d0f-978a-955c1e1952c9", "status": "released", "display_title": "4DNFI9TIAPYT.fastq.gz", "@id": "/files-fastq/4DNFI9TIAPYT/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFI9TIAPYT", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIUAJM6YE/fastqc_report.html", "status": "released", "Total Sequences": 410284237, "@id": "/quality-metrics-fastqc/383c7252-becb-4765-be6b-c42ba392a044/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "383c7252-becb-4765-be6b-c42ba392a044", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXE8G8594", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEXE8G8594", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBSIKSSGS3", "status": "released", "display_title": "4DNBSIKSSGS3", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBSIKSSGS3/", "treatments_summary": "None", "uuid": "4a1a645a-f794-4ef9-81c7-4277d1192b68", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "1d07c412-3a57-44e8-9538-aa0b4a56b43e", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/1d07c412-3a57-44e8-9538-aa0b4a56b43e/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFI6FRJ2JL", "href": "/files-processed/4DNFI6FRJ2JL/@@download/4DNFI6FRJ2JL.txt.gz", "file_size": 21365502, "uuid": "1b4ef457-2e87-4e0f-a013-85c94608df7c", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1b4ef457-2e87-4e0f-a013-85c94608df7c/4DNFI6FRJ2JL.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFI6FRJ2JL/", "md5sum": "c1a427248a75293ddb9f67b0e9755bbc", "display_title": "4DNFI6FRJ2JL.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:29.977445+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:17.509205+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEXWUNIGMP/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "e8d074d0-e784-4e7f-817a-faa3f616ccfe", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/19eaae8d-cb35-4894-9d9a-99d1d592da0f/4DNFIJN2U7EL.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "19eaae8d-cb35-4894-9d9a-99d1d592da0f", "display_title": "4DNFIJN2U7EL.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIJN2U7EL/", "href": "/files-fastq/4DNFIJN2U7EL/@@download/4DNFIJN2U7EL.fastq.gz", "md5sum": "93a553e5b1f7f16daf3fdeebda802128", "file_classification": "raw file", "file_size": 28968706311, "upload_key": "19eaae8d-cb35-4894-9d9a-99d1d592da0f/4DNFIJN2U7EL.fastq.gz", "accession": "4DNFIJN2U7EL", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "d87a3db2-c875-418c-91ac-796e5c6cf578", "status": "released", "display_title": "4DNFIDN8QYU8.fastq.gz", "@id": "/files-fastq/4DNFIDN8QYU8/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIDN8QYU8", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJN2U7EL/fastqc_report.html", "status": "released", "Total Sequences": 385234411, "@id": "/quality-metrics-fastqc/47490e7d-7074-49c8-94ab-30e7cafbf9d3/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "47490e7d-7074-49c8-94ab-30e7cafbf9d3", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 5, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/d87a3db2-c875-418c-91ac-796e5c6cf578/4DNFIDN8QYU8.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "d87a3db2-c875-418c-91ac-796e5c6cf578", "display_title": "4DNFIDN8QYU8.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIDN8QYU8/", "href": "/files-fastq/4DNFIDN8QYU8/@@download/4DNFIDN8QYU8.fastq.gz", "md5sum": "49bcc12c1c3451e73786ae0b0f6208ce", "file_classification": "raw file", "file_size": 30363458997, "upload_key": "d87a3db2-c875-418c-91ac-796e5c6cf578/4DNFIDN8QYU8.fastq.gz", "accession": "4DNFIDN8QYU8", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "19eaae8d-cb35-4894-9d9a-99d1d592da0f", "status": "released", "display_title": "4DNFIJN2U7EL.fastq.gz", "@id": "/files-fastq/4DNFIJN2U7EL/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIJN2U7EL", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIDN8QYU8/fastqc_report.html", "status": "released", "Total Sequences": 385234411, "@id": "/quality-metrics-fastqc/2dc17007-7545-41b7-9566-8e633ffa2a61/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "2dc17007-7545-41b7-9566-8e633ffa2a61", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 5, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXWUNIGMP", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEXWUNIGMP", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBS6N7HK89", "status": "released", "display_title": "4DNBS6N7HK89", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBS6N7HK89/", "treatments_summary": "None", "uuid": "b3b2a38b-b44a-4e7c-8197-01cd2b514f27", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "f4ffd78d-9e89-47a8-ac6c-dbac5fd79006", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/f4ffd78d-9e89-47a8-ac6c-dbac5fd79006/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFIZD9A13G", "href": "/files-processed/4DNFIZD9A13G/@@download/4DNFIZD9A13G.txt.gz", "file_size": 57049574, "uuid": "dcba5072-b835-4634-b2ca-40c4888022a6", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/dcba5072-b835-4634-b2ca-40c4888022a6/4DNFIZD9A13G.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFIZD9A13G/", "md5sum": "ce143d5b638761b0af893c7ff17fdf4b", "display_title": "4DNFIZD9A13G.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 5, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:29.258353+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:18.266130+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEX3DSSDC5/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "1dea6c91-df04-4288-bf7e-ec3de4b33dbb", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/52b2fd42-9a68-4e12-bf9a-0d6dd1cda890/4DNFI1YXG4J5.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "52b2fd42-9a68-4e12-bf9a-0d6dd1cda890", "display_title": "4DNFI1YXG4J5.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFI1YXG4J5/", "href": "/files-fastq/4DNFI1YXG4J5/@@download/4DNFI1YXG4J5.fastq.gz", "md5sum": "9c4826de5714f819630573cd9c88f06b", "file_classification": "raw file", "file_size": 34341109954, "upload_key": "52b2fd42-9a68-4e12-bf9a-0d6dd1cda890/4DNFI1YXG4J5.fastq.gz", "accession": "4DNFI1YXG4J5", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "cd47513a-398f-4550-bf0e-ea1651686c64", "status": "released", "display_title": "4DNFIALYPEX8.fastq.gz", "@id": "/files-fastq/4DNFIALYPEX8/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIALYPEX8", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI1YXG4J5/fastqc_report.html", "status": "released", "Total Sequences": 457418981, "@id": "/quality-metrics-fastqc/7332c284-1803-4bfc-82a3-2da4e02742e9/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "7332c284-1803-4bfc-82a3-2da4e02742e9", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 6, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/cd47513a-398f-4550-bf0e-ea1651686c64/4DNFIALYPEX8.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "cd47513a-398f-4550-bf0e-ea1651686c64", "display_title": "4DNFIALYPEX8.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIALYPEX8/", "href": "/files-fastq/4DNFIALYPEX8/@@download/4DNFIALYPEX8.fastq.gz", "md5sum": "842003ac15a48bfdbbed8ac4cffae711", "file_classification": "raw file", "file_size": 35874305841, "upload_key": "cd47513a-398f-4550-bf0e-ea1651686c64/4DNFIALYPEX8.fastq.gz", "accession": "4DNFIALYPEX8", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "52b2fd42-9a68-4e12-bf9a-0d6dd1cda890", "status": "released", "display_title": "4DNFI1YXG4J5.fastq.gz", "@id": "/files-fastq/4DNFI1YXG4J5/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFI1YXG4J5", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIALYPEX8/fastqc_report.html", "status": "released", "Total Sequences": 457418981, "@id": "/quality-metrics-fastqc/a5af0c97-b07c-4f45-957c-9b0ff2e3d29f/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "a5af0c97-b07c-4f45-957c-9b0ff2e3d29f", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 6, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEX3DSSDC5", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEX3DSSDC5", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBSJI4XIV7", "status": "released", "display_title": "4DNBSJI4XIV7", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBSJI4XIV7/", "treatments_summary": "None", "uuid": "1dbed721-4563-43a5-90c7-8cbe45ec97a7", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "5bf6164c-0fd9-4f59-89c7-79bbd2ad4bdb", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/5bf6164c-0fd9-4f59-89c7-79bbd2ad4bdb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFIX6VTUV8", "href": "/files-processed/4DNFIX6VTUV8/@@download/4DNFIX6VTUV8.txt.gz", "file_size": 59284011, "uuid": "b2e6fe82-e9e9-4aab-a61f-441df2707ad0", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b2e6fe82-e9e9-4aab-a61f-441df2707ad0/4DNFIX6VTUV8.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFIX6VTUV8/", "md5sum": "5fb500be2c65b9a9890bc41451f8b38a", "display_title": "4DNFIX6VTUV8.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 6, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:28.550993+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:18.923662+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEXBJ5AYVJ/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "fa42b5d7-574b-4fbc-80cc-aac5d8e7a28d", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/9ef8502b-01b3-4d5c-89d7-d0ccbe1c9c5b/4DNFIOUMQWGX.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "9ef8502b-01b3-4d5c-89d7-d0ccbe1c9c5b", "display_title": "4DNFIOUMQWGX.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIOUMQWGX/", "href": "/files-fastq/4DNFIOUMQWGX/@@download/4DNFIOUMQWGX.fastq.gz", "md5sum": "d1b9f6371ed1a5e02ba6483cc82ab42c", "file_classification": "raw file", "file_size": 36274190067, "upload_key": "9ef8502b-01b3-4d5c-89d7-d0ccbe1c9c5b/4DNFIOUMQWGX.fastq.gz", "accession": "4DNFIOUMQWGX", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "de4ae909-6e22-4ca5-9b55-91c80be7437c", "status": "released", "display_title": "4DNFIQYBL38B.fastq.gz", "@id": "/files-fastq/4DNFIQYBL38B/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIQYBL38B", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOUMQWGX/fastqc_report.html", "status": "released", "Total Sequences": 482884785, "@id": "/quality-metrics-fastqc/66b142f2-c163-478b-9ef0-0ab5da25aaa7/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "66b142f2-c163-478b-9ef0-0ab5da25aaa7", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 7, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/de4ae909-6e22-4ca5-9b55-91c80be7437c/4DNFIQYBL38B.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "de4ae909-6e22-4ca5-9b55-91c80be7437c", "display_title": "4DNFIQYBL38B.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIQYBL38B/", "href": "/files-fastq/4DNFIQYBL38B/@@download/4DNFIQYBL38B.fastq.gz", "md5sum": "22b07ebe8dc95becae2fc270531dd846", "file_classification": "raw file", "file_size": 37866001608, "upload_key": "de4ae909-6e22-4ca5-9b55-91c80be7437c/4DNFIQYBL38B.fastq.gz", "accession": "4DNFIQYBL38B", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "9ef8502b-01b3-4d5c-89d7-d0ccbe1c9c5b", "status": "released", "display_title": "4DNFIOUMQWGX.fastq.gz", "@id": "/files-fastq/4DNFIOUMQWGX/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIOUMQWGX", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQYBL38B/fastqc_report.html", "status": "released", "Total Sequences": 482884785, "@id": "/quality-metrics-fastqc/09f116d9-9dbd-41d8-9a52-25383867af64/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "09f116d9-9dbd-41d8-9a52-25383867af64", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 7, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXBJ5AYVJ", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEXBJ5AYVJ", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBS4OXMSQ5", "status": "released", "display_title": "4DNBS4OXMSQ5", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBS4OXMSQ5/", "treatments_summary": "None", "uuid": "860dd5da-70a5-4954-9a04-3f7e3f4c9489", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "e6bab27f-fd44-41da-97d6-7874da72ec9b", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/e6bab27f-fd44-41da-97d6-7874da72ec9b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFIGEJSK5R", "href": "/files-processed/4DNFIGEJSK5R/@@download/4DNFIGEJSK5R.txt.gz", "file_size": 65144249, "uuid": "842e90ee-a6e4-4783-89fb-5948a8d6919c", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/842e90ee-a6e4-4783-89fb-5948a8d6919c/4DNFIGEJSK5R.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFIGEJSK5R/", "md5sum": "4d9eed4f106001e26f4528bcce0d1b43", "display_title": "4DNFIGEJSK5R.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 7, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:27.837454+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:19.484826+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/experiments-seq/4DNEXDWB7B1J/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "c2370412-d2ad-4387-8649-f246fc930ad1", "files": [{"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/85d0d200-43e9-417e-ba75-2ad67918303c/4DNFIM4CNX2V.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "85d0d200-43e9-417e-ba75-2ad67918303c", "display_title": "4DNFIM4CNX2V.fastq.gz", "status": "released", "paired_end": "1", "@id": "/files-fastq/4DNFIM4CNX2V/", "href": "/files-fastq/4DNFIM4CNX2V/@@download/4DNFIM4CNX2V.fastq.gz", "md5sum": "587b293260830b24f8f76fd19e86984b", "file_classification": "raw file", "file_size": 28345283417, "upload_key": "85d0d200-43e9-417e-ba75-2ad67918303c/4DNFIM4CNX2V.fastq.gz", "accession": "4DNFIM4CNX2V", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "51ead8fc-0677-473c-b36b-2271c67e990b", "status": "released", "display_title": "4DNFIS7FYM8N.fastq.gz", "@id": "/files-fastq/4DNFIS7FYM8N/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIS7FYM8N", "file_type": "reads", "paired_end": "2", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIM4CNX2V/fastqc_report.html", "status": "released", "Total Sequences": 377822812, "@id": "/quality-metrics-fastqc/8c829356-d5a3-4e18-975b-8c7ffd03c04d/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "8c829356-d5a3-4e18-975b-8c7ffd03c04d", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 8, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/51ead8fc-0677-473c-b36b-2271c67e990b/4DNFIS7FYM8N.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "51ead8fc-0677-473c-b36b-2271c67e990b", "display_title": "4DNFIS7FYM8N.fastq.gz", "status": "released", "paired_end": "2", "@id": "/files-fastq/4DNFIS7FYM8N/", "href": "/files-fastq/4DNFIS7FYM8N/@@download/4DNFIS7FYM8N.fastq.gz", "md5sum": "2d3cdfcbf842f948f69a6d7f5ec63a42", "file_classification": "raw file", "file_size": 29662716135, "upload_key": "51ead8fc-0677-473c-b36b-2271c67e990b/4DNFIS7FYM8N.fastq.gz", "accession": "4DNFIS7FYM8N", "@type": ["FileFastq", "File", "Item"], "related_files": [{"relationship_type": "paired with", "file": {"uuid": "85d0d200-43e9-417e-ba75-2ad67918303c", "status": "released", "display_title": "4DNFIM4CNX2V.fastq.gz", "@id": "/files-fastq/4DNFIM4CNX2V/", "@type": ["FileFastq", "File", "Item"], "file_type_detailed": "reads (fastq)", "accession": "4DNFIM4CNX2V", "file_type": "reads", "paired_end": "1", "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/fastq/", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIS7FYM8N/fastqc_report.html", "status": "released", "Total Sequences": 377822812, "@id": "/quality-metrics-fastqc/298a802d-caca-43dc-8155-834313ef5105/", "display_title": "QualityMetricFastqc from 2020-05-22", "uuid": "298a802d-caca-43dc-8155-834313ef5105", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "Sequence length": "151", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "file_format": {"file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "raw file", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 8, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "accession": "4DNEXDWB7B1J", "status": "released", "display_title": "ChIA-Drop on GM19239 - 4DNEXDWB7B1J", "biosample": {"biosample_type": "immortalized cells", "@type": ["Biosample", "Item"], "accession": "4DNBSPPDN7A2", "status": "released", "display_title": "4DNBSPPDN7A2", "biosample_category": ["1000 genomes/Hap Map"], "modifications_summary": "None", "@id": "/biosamples/4DNBSPPDN7A2/", "treatments_summary": "None", "uuid": "4c7eafc8-8330-49af-8935-0e08f3715fd5", "biosource_summary": "GM19239", "biosource": [{"cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "accession": "4DNSRKH549U5", "uuid": "b350063c-d715-41eb-85d3-f75858f2de45", "display_title": "GM19239 - 4DNSRKH549U5", "@id": "/biosources/4DNSRKH549U5/", "status": "released", "cell_line": {"uuid": "a4ba07fc-3b96-4635-8ed9-5e0af39ef050", "@id": "/ontology-terms/EFO:0002789/", "term_name": "GM19239", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "GM19239", "term_id": "EFO:0002789", "preferred_name": "GM19239", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "status": "current", "display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"status": "released", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "name": "human", "scientific_name": "Homo sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@id": "/ontology-terms/CL:0000945/", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "slim_terms": [{"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "@type": ["BiosampleCellCulture", "Item"], "uuid": "026a98aa-a143-423a-84fa-8c9aa8d64d52", "display_title": "BiosampleCellCulture from 2020-05-22", "status": "released", "@id": "/biosample-cell-cultures/026a98aa-a143-423a-84fa-8c9aa8d64d52/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "badge_classification": "Warning", "warning": "Biosample Metadata Incomplete", "title": "Biosample Metadata Incomplete", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "tissue_organ_info": {"tissue_source": "B-lymphocyte", "organ_system": ["immune system"]}}, "other_processed_files": [{"description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "type": "supplementary", "title": "ChIA-DropBox and MIA-Sig Results", "files": [{"accession": "4DNFI6VGFPIE", "href": "/files-processed/4DNFI6VGFPIE/@@download/4DNFI6VGFPIE.txt.gz", "file_size": 54791812, "uuid": "05b275c2-f58e-466c-a6d5-3c05be3c5d5f", "file_type": "long range chromatin interactions", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/05b275c2-f58e-466c-a6d5-3c05be3c5d5f/4DNFI6VGFPIE.txt.gz", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "@id": "/files-processed/4DNFI6VGFPIE/", "md5sum": "3b1ccd4ccb0391d0d0822391d934ea25", "display_title": "4DNFI6VGFPIE.txt.gz", "genome_assembly": "GRCh38", "status": "released", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@type": ["FileProcessed", "File", "Item"], "file_format": {"display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "@type": ["FileFormat", "Item"], "file_format": "compressed_txt", "status": "released", "uuid": "dba26778-f40a-4561-a552-65539702ded4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"display_title": "Yijun Ruan, JAX", "@id": "/labs/yijun-ruan-lab/", "status": "current", "name": "yijun-ruan-lab", "@type": ["Lab", "Item"], "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "HindIII", "dataset": "Non-enriched ChIA-Drop on GM19239", "replicate_info": "Biorep 8, Techrep 1", "biosource_name": "GM19239", "lab_name": "Yijun Ruan, JAX"}, "last_modified": {"date_modified": "2021-12-16T07:43:27.126740+00:00"}}]}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"assay_subclassification": "DNA-DNA Multi-way Interactions", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "experiment_category": "Sequencing", "status": "released", "@type": ["ExperimentType", "Item"], "@id": "/experiment-types/chia-drop/", "display_title": "ChIA-Drop", "assay_classification": "Ligation-free 3C", "assay_subclass_short": "Ligation-free 3C", "title": "ChIA-Drop", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "experiment_categorizer": {"field": "Enzyme", "combined": "Enzyme: HindIII", "value": "HindIII"}, "last_modified": {"date_modified": "2020-06-16T17:01:20.088955+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experimentset_type": "replicate", "other_processed_files": [{"type": "supplementary", "files": [{"@type": ["FileProcessed", "File", "Item"], "status": "released", "genome_assembly": "GRCh38", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available.", "WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "file_type_detailed": "contact matrix (mcool)", "href": "/files-processed/4DNFI81RQ431/@@download/4DNFI81RQ431.mcool", "file_type": "contact matrix", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@id": "/file-formats/mcool/", "status": "released", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "3902efc1-3589-4472-8090-cc871cf0e9fe", "accession": "4DNFI81RQ431", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3902efc1-3589-4472-8090-cc871cf0e9fe/4DNFI81RQ431.mcool", "@id": "/files-processed/4DNFI81RQ431/", "higlass_uid": "7ea534bf-83de-42f6-92f0-431696cbc28a", "file_size": 338086540, "md5sum": "233040e3d443e4080e794c83631e7df3", "display_title": "4DNFI81RQ431.mcool", "quality_metric": {"@id": "/quality-metrics-mcool/6550f799-e175-4c2e-8695-5b14c3ab8f2c/", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "WARN", "uuid": "6550f799-e175-4c2e-8695-5b14c3ab8f2c", "display_title": "QualityMetricMcool from 2021-05-21", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "5000; 10000; 25000; 50000; 100000; 250000; 500000; 1000000; 2500000", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "contributing_labs": [{"display_title": "Yijun Ruan, JAX", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/yijun-ruan-lab/", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "name": "yijun-ruan-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}], "lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "name": "4dn-dcic-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"uuid": "013554ab-7955-4d48-95a5-b383c512f7b0", "@id": "/higlass-view-configs/013554ab-7955-4d48-95a5-b383c512f7b0/", "status": "released", "display_title": "4DNFI81RQ431 - contact matrix for GM19239 ChIA-Drop HindIII", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "last_modified": {"date_modified": "2023-08-25T17:50:12.951840+00:00"}, "track_and_facet_info": {"dataset": "Non-enriched ChIA-Drop on GM19239", "experimental_lab": "Yijun Ruan, JAX", "replicate_info": "merged replicates", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "experiment_type": "ChIA-Drop", "assay_info": "HindIII", "biosource_name": "GM19239", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for GM19239 ChIA-Drop HindIII"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "ChIA-DropBox and MIA-Sig Results", "description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization.", "higlass_view_config": {"description": "Supplementary Files (ChIA-DropBox and MIA-Sig Results) for 4DNESXGXZEZ6 (Replicates of non-enriched ChIA-Drop on GM19239 cells.): 4DNFI81RQ431", "status": "released", "@id": "/higlass-view-configs/e3ac2d2f-ee8c-4545-815d-05bee4a09b31/", "uuid": "e3ac2d2f-ee8c-4545-815d-05bee4a09b31", "display_title": "4DNESXGXZEZ6 - ChIA-DropBox and MIA-Sig Results", "@type": ["HiglassViewConfig", "UserContent", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}, "last_modified": {"date_modified": "2020-10-30T16:17:20.052412+00:00"}}}], "@id": "/experiment-set-replicates/4DNESXGXZEZ6/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "e881357c-2679-4b6a-a97d-373069a6f458", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESXGXZEZ6", "external_references": [], "pubs_using": [], "publications_of_set": [], "number_of_experiments": 8, "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBS76PQJ1M/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSDFLXDEE/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSW5FE37E/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSIKSSGS3/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBS6N7HK89/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSJI4XIV7/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBS4OXMSQ5/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}, {"parent": "/biosamples/4DNBSPPDN7A2/", "embedded_path": "experiments_in_set.biosample.badges", "item": {"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}