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IGVFDS3642NEVV

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS3642NEVV/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3642NEVV",
    "aliases": [
        "bradley-bernstein:scRNA Lib 25",
        "buenrostro-bernstein:scRNA Lib 25"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002631/",
        "assay_slims": [
            "gene expression"
        ],
        "status": "released",
        "term_name": "single-cell RNA sequencing assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released primary cell [IGVFSM7251TZFC](/primary-cells/IGVFSM7251TZFC/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM7251TZFC/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM7251TZFC](/primary-cells/IGVFSM7251TZFC/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_sample_missing_publication",
                "path": "/primary-cells/IGVFSM7251TZFC/"
            },
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_file_set_missing_publication",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has sequence file(s): [IGVFFI4059PDDO](/sequence-files/IGVFFI4059PDDO/), [IGVFFI8043LYVQ](/sequence-files/IGVFFI8043LYVQ/), [IGVFFI1683TOVH](/sequence-files/IGVFFI1683TOVH/), [IGVFFI6116NHMX](/sequence-files/IGVFFI6116NHMX/), [IGVFFI3586QVZS](/sequence-files/IGVFFI3586QVZS/), [IGVFFI7539ZPVB](/sequence-files/IGVFFI7539ZPVB/), [IGVFFI6822JJVL](/sequence-files/IGVFFI6822JJVL/), [IGVFFI3227UMSV](/sequence-files/IGVFFI3227UMSV/), [IGVFFI3532IJYB](/sequence-files/IGVFFI3532IJYB/), [IGVFFI1659TORI](/sequence-files/IGVFFI1659TORI/), [IGVFFI9739WHAC](/sequence-files/IGVFFI9739WHAC/), [IGVFFI7671SQNA](/sequence-files/IGVFFI7671SQNA/), [IGVFFI4018PRYW](/sequence-files/IGVFFI4018PRYW/), [IGVFFI6026XURL](/sequence-files/IGVFFI6026XURL/), [IGVFFI6372XVNE](/sequence-files/IGVFFI6372XVNE/), [IGVFFI6738DQFD](/sequence-files/IGVFFI6738DQFD/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI4059PDDO](/sequence-files/IGVFFI4059PDDO/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI8043LYVQ](/sequence-files/IGVFFI8043LYVQ/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI1683TOVH](/sequence-files/IGVFFI1683TOVH/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI6116NHMX](/sequence-files/IGVFFI6116NHMX/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI3586QVZS](/sequence-files/IGVFFI3586QVZS/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI7539ZPVB](/sequence-files/IGVFFI7539ZPVB/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI6822JJVL](/sequence-files/IGVFFI6822JJVL/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI3227UMSV](/sequence-files/IGVFFI3227UMSV/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI3532IJYB](/sequence-files/IGVFFI3532IJYB/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI1659TORI](/sequence-files/IGVFFI1659TORI/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI9739WHAC](/sequence-files/IGVFFI9739WHAC/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI7671SQNA](/sequence-files/IGVFFI7671SQNA/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI4018PRYW](/sequence-files/IGVFFI4018PRYW/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI6026XURL](/sequence-files/IGVFFI6026XURL/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI6372XVNE](/sequence-files/IGVFFI6372XVNE/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has a sequence file [IGVFFI6738DQFD](/sequence-files/IGVFFI6738DQFD/) missing `read_names`. Sequence files are expected to have read names.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_single_cell_read_names",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_strand_specificity",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS3642NEVV](/measurement-sets/IGVFDS3642NEVV/) has an `assay_term` of single-cell RNA sequencing assay but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_onlist",
                "path": "/measurement-sets/IGVFDS3642NEVV/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011986/",
        "component": "mapping",
        "contact_pi": {
            "@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
            "title": "Jason Buenrostro"
        },
        "title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
    },
    "control_for": [],
    "controlled_access": false,
    "creation_timestamp": "2024-02-12T21:12:25.554718+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO9431XGDA/",
            "accession": "IGVFDO9431XGDA",
            "aliases": [
                "bradley-bernstein:Donor 1506",
                "buenrostro-bernstein:Donor 1506"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI4059PDDO/",
            "accession": "IGVFFI4059PDDO",
            "aliases": [
                "bradley-bernstein:SS-LS_2478_R2",
                "buenrostro-bernstein:SS-LS_2478_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:15.596136+00:00",
            "file_format": "fastq",
            "file_size": 1237590402,
            "href": "/sequence-files/IGVFFI4059PDDO/@@download/IGVFFI4059PDDO.fastq.gz",
            "md5sum": "2abe180a6d285536c378330f5615e4ab",
            "s3_uri": "s3://igvf-files/2024/02/12/cba02e05-fe95-4c6e-b213-2a3588198b0c/IGVFFI4059PDDO.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-50_L3_SS-PKR-5_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8043LYVQ/",
            "accession": "IGVFFI8043LYVQ",
            "aliases": [
                "bradley-bernstein:SS-LS_1424_R2",
                "buenrostro-bernstein:SS-LS_1424_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:23:37.951252+00:00",
            "file_format": "fastq",
            "file_size": 2684091065,
            "href": "/sequence-files/IGVFFI8043LYVQ/@@download/IGVFFI8043LYVQ.fastq.gz",
            "md5sum": "869101c5e26625b19ffd50e01d79d106",
            "s3_uri": "s3://igvf-files/2024/02/12/2c58af7c-e893-43ac-b44c-6976d7329239/IGVFFI8043LYVQ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1113_L1_SS-PKR-5_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1683TOVH/",
            "accession": "IGVFFI1683TOVH",
            "aliases": [
                "bradley-bernstein:SS-LS_2574_R2",
                "buenrostro-bernstein:SS-LS_2574_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:52.574023+00:00",
            "file_format": "fastq",
            "file_size": 1219838124,
            "href": "/sequence-files/IGVFFI1683TOVH/@@download/IGVFFI1683TOVH.fastq.gz",
            "md5sum": "1b0e0cef74672d3b6a57756130da7832",
            "s3_uri": "s3://igvf-files/2024/02/12/f4e84654-5551-4d54-9fb2-72df674faf53/IGVFFI1683TOVH.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-50_L4_SS-PKR-5_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6116NHMX/",
            "accession": "IGVFFI6116NHMX",
            "aliases": [
                "bradley-bernstein:SS-LS_1424_R1",
                "buenrostro-bernstein:SS-LS_1424_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:23:36.772945+00:00",
            "file_format": "fastq",
            "file_size": 1006491125,
            "href": "/sequence-files/IGVFFI6116NHMX/@@download/IGVFFI6116NHMX.fastq.gz",
            "md5sum": "a5876d008c9ccfb138f9c928ebd76d55",
            "s3_uri": "s3://igvf-files/2024/02/12/2c25f08b-c7ee-429d-996a-29b4ec3c1f3a/IGVFFI6116NHMX.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1113_L1_SS-PKR-5_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3586QVZS/",
            "accession": "IGVFFI3586QVZS",
            "aliases": [
                "bradley-bernstein:SS-LS_1520_R2",
                "buenrostro-bernstein:SS-LS_1520_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:28:04.936930+00:00",
            "file_format": "fastq",
            "file_size": 2731822055,
            "href": "/sequence-files/IGVFFI3586QVZS/@@download/IGVFFI3586QVZS.fastq.gz",
            "md5sum": "fd30f07e0474ff19d4f2f58fae07acd7",
            "s3_uri": "s3://igvf-files/2024/02/12/cc75f352-62f6-4622-9705-cbb1a43bba60/IGVFFI3586QVZS.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1113_L2_SS-PKR-5_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7539ZPVB/",
            "accession": "IGVFFI7539ZPVB",
            "aliases": [
                "bradley-bernstein:SS-LS_2478_R1",
                "buenrostro-bernstein:SS-LS_2478_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:14.571700+00:00",
            "file_format": "fastq",
            "file_size": 524532068,
            "href": "/sequence-files/IGVFFI7539ZPVB/@@download/IGVFFI7539ZPVB.fastq.gz",
            "md5sum": "c6455ebae89127d61b41b38922c5af3e",
            "s3_uri": "s3://igvf-files/2024/02/12/b2ba4bc7-f8de-4338-9303-95973bb4600f/IGVFFI7539ZPVB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-50_L3_SS-PKR-5_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6822JJVL/",
            "accession": "IGVFFI6822JJVL",
            "aliases": [
                "bradley-bernstein:SS-LS_2574_R1",
                "buenrostro-bernstein:SS-LS_2574_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:51.575109+00:00",
            "file_format": "fastq",
            "file_size": 515834499,
            "href": "/sequence-files/IGVFFI6822JJVL/@@download/IGVFFI6822JJVL.fastq.gz",
            "md5sum": "8dc3b29f8d13f5b49e7531640e7159bc",
            "s3_uri": "s3://igvf-files/2024/02/12/c9c741e1-dddd-4544-af17-cf4adc47f5e6/IGVFFI6822JJVL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-50_L4_SS-PKR-5_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3227UMSV/",
            "accession": "IGVFFI3227UMSV",
            "aliases": [
                "bradley-bernstein:SS-LS_1520_R1",
                "buenrostro-bernstein:SS-LS_1520_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:28:03.995246+00:00",
            "file_format": "fastq",
            "file_size": 1025974049,
            "href": "/sequence-files/IGVFFI3227UMSV/@@download/IGVFFI3227UMSV.fastq.gz",
            "md5sum": "a77f3079be27f469d2f6d200d720c2e8",
            "s3_uri": "s3://igvf-files/2024/02/12/029eddfb-15a8-469e-a650-cbc80cd475d6/IGVFFI3227UMSV.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008637/",
                "status": "released",
                "term_name": "Illumina NovaSeq 6000"
            },
            "status": "released",
            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1113_L2_SS-PKR-5_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3532IJYB/",
            "accession": "IGVFFI3532IJYB",
            "aliases": [
                "bradley-bernstein:SS-LS_1616_R1",
                "buenrostro-bernstein:SS-LS_1616_R1"
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