{"lab": {"correspondence": [{"contact_email": "eWluLnNoZW5AdWNzZi5lZHU=", "@id": "/users/f9ea2a42-c642-4496-9276-6b8c4c3a1225/", "display_title": "Yin Shen"}], "display_title": "Yin Shen, UCSF", "status": "current", "@type": ["Lab", "Item"], "title": "Yin Shen, UCSF", "uuid": "cb39c51c-289a-4c6e-bfaa-46e61572daf5", "@id": "/labs/yin-shen-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cb39c51c-289a-4c6e-bfaa-46e61572daf5"]}}, "tags": ["strandedness_verified"], "award": {"uuid": "3a0877de-6aed-413f-811f-a2d0961d2f57", "display_title": "CHARTING THE 3D EPIGENOME IN HUMAN BRAIN DEVELOPMENT AND DISEASES", "@type": ["Award", "Item"], "@id": "/awards/1U01DA052713-01/", "project": "4DN", "description": "OFHHD: Cis-regulatory elements control Cell-type-specific gene regulation via looping with their targeting genes. Therefore, mapping the 3D chromatin interactions between promoters and cis-regulatory elements will be pivotal to understand the functions of regulatory regions. Besides, many genetic variants associated with neuropsychiatric diseases reside in the putative cis-regulatory elements. They may contribute to disease by affecting regulatory sequences function, but the exact mechanisms of how they contribute to diseases via gene regulation remain unknown. Here, we aim to make substantial advances in understanding how the 3D epigenome contributes to brain development and diseases by mapping and analyzing the dynamic changes during the human prefrontal cortex development. We will first map transcriptome, chromatin accessibility, and 3D chromatin loops in six distinct cell types from the developing prefrontal cortex and perform an integrative analysis to interrogate how chromatin interaction control gene expression and development. Second, we will integrate the 3D epigenomic datasets with medical genetics resources to gain insights into cell types, genomic loci, and biological pathways that are causal to diseases, link GWAS SNPs with their target genes. Third, to establish cell-type-specific functional links between chromatin loops and target gene expression, we will test the biological consequences of distal regulatory regions interacting with promoters in iPSC models and primary cells. Our project will reveal new insight into the biological functions of the 3D epigenome in brain development and diseases.", "status": "current", "name": "1U01DA052713-01", "center_title": "OFHHD - Shen", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type_detailed": "reads (fastq)", "accession": "4DNFIT99AD7T", "href": "/files-fastq/4DNFIT99AD7T/@@download/4DNFIT99AD7T.fastq.gz", "file_classification": "raw file", "file_size": 1762392856, "upload_key": "b234cd05-b532-4da1-bc23-d5b345a75145/4DNFIT99AD7T.fastq.gz", "@id": "/files-fastq/4DNFIT99AD7T/", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIT99AD7T.fastq.gz", "status": "restricted", "uuid": "b234cd05-b532-4da1-bc23-d5b345a75145", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIPJFRTW1.fastq.gz", "@id": "/files-fastq/4DNFIPJFRTW1/", "file_type": "reads", "accession": "4DNFIPJFRTW1", "status": "restricted", "uuid": "bcda3d3c-454f-41e7-bcb5-fbd759c78ed2", "file_type_detailed": "reads (fastq)", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"@id": "/quality-metrics-fastqc/beb6e4c6-a36c-42f5-b869-932b4738fdb5/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT99AD7T/fastqc_report.html", "display_title": "QualityMetricFastqc from 2025-05-13", "Total Sequences": 32377269, "uuid": "beb6e4c6-a36c-42f5-b869-932b4738fdb5", "status": "released", "overall_quality_status": "PASS", "Sequence length": "101", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"file_type_detailed": "reads (fastq)", "accession": "4DNFIPJFRTW1", "href": "/files-fastq/4DNFIPJFRTW1/@@download/4DNFIPJFRTW1.fastq.gz", "file_classification": "raw file", "file_size": 1827266796, "upload_key": "bcda3d3c-454f-41e7-bcb5-fbd759c78ed2/4DNFIPJFRTW1.fastq.gz", "@id": "/files-fastq/4DNFIPJFRTW1/", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIPJFRTW1.fastq.gz", "status": "restricted", "uuid": "bcda3d3c-454f-41e7-bcb5-fbd759c78ed2", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIT99AD7T.fastq.gz", "@id": "/files-fastq/4DNFIT99AD7T/", "file_type": "reads", "accession": "4DNFIT99AD7T", "status": "restricted", "uuid": "b234cd05-b532-4da1-bc23-d5b345a75145", "file_type_detailed": "reads (fastq)", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "quality_metric": {"@id": "/quality-metrics-fastqc/775e0e35-77b5-4b5c-b741-e60022a84844/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIPJFRTW1/fastqc_report.html", "display_title": "QualityMetricFastqc from 2025-05-13", "Total Sequences": 32377269, "uuid": "775e0e35-77b5-4b5c-b741-e60022a84844", "status": "released", "overall_quality_status": "PASS", "Sequence length": "101", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@type": ["FileFormat", "Item"], "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "status": "released", "aliases": ["yin-shen-lab:experiment_JJ029-ARK-2021-009-rnaseq-MG_B1_T1"], "molecule": "total RNA", "protocol": {"@id": "/protocols/1075b676-7d73-495e-a2ec-2780a1090ea1/", "@type": ["Protocol", "Item"], "display_title": "Shen lab RNA-seq protocol", "uuid": "1075b676-7d73-495e-a2ec-2780a1090ea1", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXMXUYRII", "biosample": {"biosample_type": "primary cells", "display_title": "4DNBSJ9ZW7W6", "status": "released", "biosource_summary": "cortical microglia", "@type": ["Biosample", "Item"], "accession": "4DNBSJ9ZW7W6", "@id": "/biosamples/4DNBSJ9ZW7W6/", "treatments_summary": "None", "uuid": "ffecaed2-2a67-4b50-aacb-ace1f976fa2d", "modifications_summary": "None", "biosource": [{"lab": {"status": "current", "uuid": "cb39c51c-289a-4c6e-bfaa-46e61572daf5", "@type": ["Lab", "Item"], "@id": "/labs/yin-shen-lab/", "display_title": "Yin Shen, UCSF", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cb39c51c-289a-4c6e-bfaa-46e61572daf5"]}}, "award": {"uuid": "3a0877de-6aed-413f-811f-a2d0961d2f57", "@type": ["Award", "Item"], "@id": "/awards/1U01DA052713-01/", "status": "current", "display_title": "CHARTING THE 3D EPIGENOME IN HUMAN BRAIN DEVELOPMENT AND DISEASES", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"slim_terms": [{"@id": "/ontology-terms/UBERON:0001017/", "uuid": "111136bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "central nervous system", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000955/", "uuid": "111170bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "brain", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000924/", "uuid": "111119bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "ectoderm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_name": "cortex of cerebral lobe", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0016529", "status": "released", "preferred_name": "cortex of cerebral lobe", "uuid": "2656a9bc-491a-4df4-a8f2-24badaebd817", "@id": "/ontology-terms/UBERON:0016529/", "display_title": "cortex of cerebral lobe", "synonyms": ["cortex of lobe of cerebral hemisphere", "cortex of cerebral hemisphere lobe"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["yin-shen-lab:ARK-2021-009-MG"], "accession": "4DNSRR2NVFRE", "cell_line": {"synonyms": ["microglia", "hortega cells", "brain-resident macrophage", "microgliocyte"], "@id": "/ontology-terms/CL:0000129/", "status": "released", "preferred_name": "microglial cell", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "display_title": "immune system", "uuid": "111133bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0002405/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "mesoderm", "uuid": "111120bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0000926/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "ectoderm", "uuid": "111119bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0000924/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "display_title": "central nervous system", "uuid": "111136bc-8535-4448-903e-854af460a233", "status": "released", "@id": "/ontology-terms/UBERON:0001017/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_id": "CL:0000129", "@type": ["OntologyTerm", "Item"], "display_title": "microglial cell", "uuid": "cbb152ad-dd39-4537-83e5-39abd16e8d29", "term_name": "microglial cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@id": "/individuals-human/4DNIN4YKCCSR/", "uuid": "e9bf08fe-49a7-40f7-81fd-2dbd80606df8", "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNIN4YKCCSR", "protected_data": true, "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "PU1+ microglia from cortex of donor ARK-2021-009", "date_created": "2025-05-05T16:43:24.990028+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2026-04-29T14:06:10.638818+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2026-04-29", "schema_version": "2", "project_release": "2026-04-29", "override_biosource_name": "cortical microglia", "@id": "/biosources/4DNSRR2NVFRE/", "@type": ["Biosource", "Item"], "uuid": "045358b8-67fa-4281-a0cd-41a1f8317961", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "cortical microglia - 4DNSRR2NVFRE", "external_references": [], "biosource_name": "cortical microglia", "biosource_category": ["Primary Cells"], "organism": {"name": "human", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "display_title": "H. sapiens", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "sop_mapping": {"has_sop": "No"}, "date_created": "2025-05-05T20:10:16.951697+00:00", "strandedness": "reverse", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2026-04-29T13:30:18.167276+00:00"}, "public_release": "2026-04-29", "schema_version": "5", "experiment_type": {"status": "released", "@type": ["ExperimentType", "Item"], "experiment_category": "Sequencing", "assay_subclass_short": "Transcription", "@id": "/experiment-types/rna-seq/", "display_title": "RNA-seq", "title": "RNA-seq", "uuid": "19f848e6-7c52-4b8b-8aa8-e82ea0a968ce", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"href": "/files-processed/4DNFIXACS5PT/@@download/4DNFIXACS5PT.bam", "file_classification": "processed file", "upload_key": "1dc14439-e1aa-4aa4-bea9-44973b23895f/4DNFIXACS5PT.bam", "file_type": "read positions", "@id": "/files-processed/4DNFIXACS5PT/", "display_title": "4DNFIXACS5PT.bam", "file_format": {"@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "file_format": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "restricted", "accession": "4DNFIXACS5PT", "file_type_detailed": "read positions (bam)", "uuid": "1dc14439-e1aa-4aa4-bea9-44973b23895f", "file_size": 3289699386, "quality_metric": {"status": "released", "uuid": "776f315c-47b5-42b9-ace4-1c89639e479c", "overall_quality_status": "PASS", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "display_title": "QualityMetricRnaseq from 2025-06-18", "@id": "/quality-metrics-rnaseq/776f315c-47b5-42b9-ace4-1c89639e479c/", "quality_metric_summary": [{"title": "Total mapped reads (genome)", "value": "30942666", "numberType": "integer"}, {"title": "Total uniquely mapped reads (genome)", "value": "30042926", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yin Shen, UCSF", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on fetal cortical glial cells", "condition": "ARK-2021-009 MG", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cortical microglia", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIHA832F6/@@download/4DNFIHA832F6.bw", "file_classification": "processed file", "upload_key": "226cc724-32cd-42d3-9203-f6177498cdcf/4DNFIHA832F6.bw", "file_type": "read counts (plus)", "@id": "/files-processed/4DNFIHA832F6/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/226cc724-32cd-42d3-9203-f6177498cdcf/4DNFIHA832F6.bw", "display_title": "4DNFIHA832F6.bw", "file_format": {"@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "file_format": "bw", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIHA832F6", "file_type_detailed": "read counts (plus) (bw)", "uuid": "226cc724-32cd-42d3-9203-f6177498cdcf", "file_size": 166922212, "track_and_facet_info": {"experimental_lab": "Yin Shen, UCSF", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on fetal cortical glial cells", "condition": "ARK-2021-009 MG", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cortical microglia", "lab_name": "4DN DCIC, HMS", "track_title": "read counts (plus) for cortical microglia RNA-seq"}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIHA832F6 - read counts (plus) for cortical microglia RNA-seq", "uuid": "71292553-f592-45e7-ac35-c03ff889caa1", "@id": "/higlass-view-configs/71292553-f592-45e7-ac35-c03ff889caa1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFITT2C5OL/@@download/4DNFITT2C5OL.bw", "file_classification": "processed file", "upload_key": "d1af02c4-01c7-4df6-a053-9bd7912d6b7e/4DNFITT2C5OL.bw", "file_type": "read counts (minus)", "@id": "/files-processed/4DNFITT2C5OL/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d1af02c4-01c7-4df6-a053-9bd7912d6b7e/4DNFITT2C5OL.bw", "display_title": "4DNFITT2C5OL.bw", "file_format": {"@id": "/file-formats/bw/", "@type": ["FileFormat", "Item"], "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "file_format": "bw", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFITT2C5OL", "file_type_detailed": "read counts (minus) (bw)", "uuid": "d1af02c4-01c7-4df6-a053-9bd7912d6b7e", "file_size": 156953957, "track_and_facet_info": {"experimental_lab": "Yin Shen, UCSF", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on fetal cortical glial cells", "condition": "ARK-2021-009 MG", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cortical microglia", "lab_name": "4DN DCIC, HMS", "track_title": "read counts (minus) for cortical microglia RNA-seq"}, "static_content": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFITT2C5OL - read counts (minus) for cortical microglia RNA-seq", "uuid": "48ef624b-098c-41f3-be2f-6f719b3b3549", "@id": "/higlass-view-configs/48ef624b-098c-41f3-be2f-6f719b3b3549/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIKZDR7AA/@@download/4DNFIKZDR7AA.tsv", "file_classification": "processed file", "upload_key": "da591b8a-9f80-4c31-9d27-5e793cfb7189/4DNFIKZDR7AA.tsv", "file_type": "gene expression", "@id": "/files-processed/4DNFIKZDR7AA/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/da591b8a-9f80-4c31-9d27-5e793cfb7189/4DNFIKZDR7AA.tsv", "display_title": "4DNFIKZDR7AA.tsv", "file_format": {"@id": "/file-formats/tsv/", "@type": ["FileFormat", "Item"], "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "display_title": "tsv", "file_format": "tsv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIKZDR7AA", "file_type_detailed": "gene expression (tsv)", "uuid": "da591b8a-9f80-4c31-9d27-5e793cfb7189", "file_size": 10792748, "quality_metric": {"status": "released", "uuid": "3a2a0f6c-ab5c-4330-ad99-4f57d2c0995b", "overall_quality_status": "PASS", "@type": ["QualityMetricRnaseq", "QualityMetric", "Item"], "display_title": "QualityMetricRnaseq from 2025-06-18", "@id": "/quality-metrics-rnaseq/3a2a0f6c-ab5c-4330-ad99-4f57d2c0995b/", "quality_metric_summary": [{"title": "Reads mapped to protein-coding genes", "value": "9256332", "numberType": "integer"}, {"title": "Reads mapped to rRNA", "value": "26", "numberType": "integer"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Yin Shen, UCSF", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on fetal cortical glial cells", "condition": "ARK-2021-009 MG", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cortical microglia", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"href": "/files-processed/4DNFIJ6WAQQ6/@@download/4DNFIJ6WAQQ6.tsv", "file_classification": "processed file", "upload_key": "f8306303-6c65-4033-8652-1b7149555e1c/4DNFIJ6WAQQ6.tsv", "file_type": "isoform expression", "@id": "/files-processed/4DNFIJ6WAQQ6/", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f8306303-6c65-4033-8652-1b7149555e1c/4DNFIJ6WAQQ6.tsv", "display_title": "4DNFIJ6WAQQ6.tsv", "file_format": {"@id": "/file-formats/tsv/", "@type": ["FileFormat", "Item"], "uuid": "5e8f64b8-6323-410a-8af2-05aba0472f8e", "display_title": "tsv", "file_format": "tsv", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIJ6WAQQ6", "file_type_detailed": "isoform expression (tsv)", "uuid": "f8306303-6c65-4033-8652-1b7149555e1c", "file_size": 31097624, "track_and_facet_info": {"experimental_lab": "Yin Shen, UCSF", "experiment_type": "RNA-seq", "experiment_bucket": "processed file", "dataset": "RNA-seq on fetal cortical glial cells", "condition": "ARK-2021-009 MG", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cortical microglia", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2026-04-29", "library_prep_kit": "KAPA RNA HyperPrep Kit with RiboErase (HMR)", "biosample_quantity": 1000000.0, "biosample_quantity_units": "cells", "library_preparation_date": "2021-11-19", "@id": "/experiments-seq/4DNEXMXUYRII/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "f063c31e-a906-41aa-931c-94b5536d7dfe", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "RNA-seq on cortical microglia - 4DNEXMXUYRII", "external_references": [], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESBLQ1ADP/", "uuid": "6bb407c2-a61f-4bdb-a14e-4146ddbde861", "experimentset_type": "replicate", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESBLQ1ADP", "display_title": "4DNESBLQ1ADP", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_exp": [], "experiment_categorizer": {"field": "Default", "value": null}, "experiment_summary": "RNA-seq on cortical microglia", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}