IGVFFI9362JSBS

released
validated
{
    "@context": "/terms/",
    "@id": "/tabular-files/IGVFFI9362JSBS/",
    "@type": [
        "TabularFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI9362JSBS",
    "aliases": [
        "buenrostro-bernstein:IGVFDS4147RERW_fragments"
    ],
    "analysis_step_version": "/analysis-step-versions/39c0498d-91f6-42de-8896-2fab1403f032/",
    "assay_titles": [
        "SHARE-seq"
    ],
    "assembly": "GRCm39",
    "audit": {},
    "award": {
        "@id": "/awards/HG011986/",
        "component": "mapping"
    },
    "barcode_map_for": [],
    "checkfiles_version": "v20",
    "content_md5sum": "0274dc6d7fe1b948eaa76061935e6774",
    "content_type": "fragments",
    "controlled_access": false,
    "creation_timestamp": "2025-03-27T01:18:02.983571+00:00",
    "derived_from": [
        "/sequence-files/IGVFFI7404RARD/",
        "/sequence-files/IGVFFI2288NVQQ/",
        "/sequence-files/IGVFFI4401IERR/",
        "/sequence-files/IGVFFI9611UAWB/",
        "/sequence-files/IGVFFI7093KEGU/",
        "/sequence-files/IGVFFI0716KABP/",
        "/sequence-files/IGVFFI2233SDVD/",
        "/sequence-files/IGVFFI2741HIJM/",
        "/sequence-files/IGVFFI5516VUUY/",
        "/sequence-files/IGVFFI3550CIIB/",
        "/sequence-files/IGVFFI5827ESIJ/",
        "/sequence-files/IGVFFI2873EEMS/",
        "/configuration-files/IGVFFI6435JSJB/",
        "/configuration-files/IGVFFI5074EAGI/",
        "/configuration-files/IGVFFI5466LSXE/",
        "/configuration-files/IGVFFI7894WFLU/",
        "/configuration-files/IGVFFI9449ARSM/",
        "/configuration-files/IGVFFI9636XHPK/"
    ],
    "file_format": "bed",
    "file_format_specifications": [
        {
            "@id": "/documents/db2a6dd0-cc1d-439e-a610-f9f1d04cfd82/",
            "description": "Specification of fragment file generated by https://github.com/IGVF/single-cell-pipeline"
        }
    ],
    "file_format_type": "bed3+",
    "file_set": {
        "@id": "/analysis-sets/IGVFDS4147RERW/",
        "@type": [
            "AnalysisSet",
            "FileSet",
            "Item"
        ],
        "accession": "IGVFDS4147RERW",
        "data_use_limitation_summaries": [
            "no certificate"
        ],
        "file_set_type": "intermediate analysis",
        "samples": [
            {
                "@id": "/tissues/IGVFSM9781HISX/",
                "@type": [
                    "Tissue",
                    "Biosample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM9781HISX",
                "classifications": [
                    "tissue"
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/UBERON_0000955/",
                        "status": "released",
                        "term_name": "brain"
                    }
                ],
                "status": "released",
                "summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 131)",
                "taxa": "Mus musculus"
            }
        ],
        "status": "released",
        "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)"
    },
    "file_size": 886785152,
    "filtered": false,
    "gene_list_for": [],
    "href": "/tabular-files/IGVFFI9362JSBS/@@download/IGVFFI9362JSBS.bed.gz",
    "input_file_for": [
        "/index-files/IGVFFI7584MFEP/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jason-buenrostro/",
        "title": "Jason Buenrostro, Broad"
    },
    "loci_list_for": [],
    "md5sum": "46121789e47b2b186cf55dfa7c8bb9b3",
    "primer_design_for": [],
    "quality_metrics": [
        "/single-cell-atac-seq-quality-metrics/8b3f2bbc-1df1-4180-91d5-4508817cf107/"
    ],
    "release_timestamp": "2025-05-07T20:35:09.763427+00:00",
    "s3_uri": "s3://igvf-files/2025/03/27/7c1fbd9d-71af-416f-88cd-1bcf56fa5e94/IGVFFI9362JSBS.bed.gz",
    "schema_version": "15",
    "status": "released",
    "submitted_by": {
        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
        "title": "Siddarth Wekhande"
    },
    "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/67efe196-b6fa-4d32-adf0-323869bb96b7/call-atac/wf_atac/ab98e91d-a104-4f77-b7d9-4a764546d96e/call-generate_fragments/SS-PKR-131.fragments.tsv.gz",
    "summary": "GRCm39 unfiltered fragments",
    "upload_status": "validated",
    "uuid": "7c1fbd9d-71af-416f-88cd-1bcf56fa5e94",
    "workflow": {
        "@id": "/workflows/IGVFWF7365VWQV/",
        "name": "igvf single cell uniform pipeline",
        "uniform_pipeline": true
    }
}