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IGVFDS9698PDND

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS9698PDND/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9698PDND",
    "aliases": [
        "bradley-bernstein:scRNA Lib 27",
        "buenrostro-bernstein:scRNA Lib 27"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002631/",
        "assay_slims": [
            "gene expression"
        ],
        "status": "released",
        "term_name": "single-cell RNA sequencing assay"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "mismatched status",
                "detail": "Released primary cell [IGVFSM9099ITYD](/primary-cells/IGVFSM9099ITYD/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM9099ITYD/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM9099ITYD](/primary-cells/IGVFSM9099ITYD/) 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/IGVFSM9099ITYD/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has sequence file(s): [IGVFFI1766EGWZ](/sequence-files/IGVFFI1766EGWZ/), [IGVFFI1914CZDQ](/sequence-files/IGVFFI1914CZDQ/), [IGVFFI7105ZLWV](/sequence-files/IGVFFI7105ZLWV/), [IGVFFI0445CBFR](/sequence-files/IGVFFI0445CBFR/), [IGVFFI2985KCGA](/sequence-files/IGVFFI2985KCGA/), [IGVFFI2001SFNQ](/sequence-files/IGVFFI2001SFNQ/), [IGVFFI8332UVED](/sequence-files/IGVFFI8332UVED/), [IGVFFI1009RQOH](/sequence-files/IGVFFI1009RQOH/), [IGVFFI9434DEGG](/sequence-files/IGVFFI9434DEGG/), [IGVFFI0852ACVD](/sequence-files/IGVFFI0852ACVD/), [IGVFFI6330JJWL](/sequence-files/IGVFFI6330JJWL/), [IGVFFI3820NYHT](/sequence-files/IGVFFI3820NYHT/), [IGVFFI7484UJVI](/sequence-files/IGVFFI7484UJVI/), [IGVFFI9898PMZZ](/sequence-files/IGVFFI9898PMZZ/), [IGVFFI7124VTBR](/sequence-files/IGVFFI7124VTBR/), [IGVFFI1864UPQB](/sequence-files/IGVFFI1864UPQB/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI1766EGWZ](/sequence-files/IGVFFI1766EGWZ/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI1914CZDQ](/sequence-files/IGVFFI1914CZDQ/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI7105ZLWV](/sequence-files/IGVFFI7105ZLWV/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI0445CBFR](/sequence-files/IGVFFI0445CBFR/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI2985KCGA](/sequence-files/IGVFFI2985KCGA/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI2001SFNQ](/sequence-files/IGVFFI2001SFNQ/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI8332UVED](/sequence-files/IGVFFI8332UVED/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI1009RQOH](/sequence-files/IGVFFI1009RQOH/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI9434DEGG](/sequence-files/IGVFFI9434DEGG/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI0852ACVD](/sequence-files/IGVFFI0852ACVD/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI6330JJWL](/sequence-files/IGVFFI6330JJWL/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI3820NYHT](/sequence-files/IGVFFI3820NYHT/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI7484UJVI](/sequence-files/IGVFFI7484UJVI/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI9898PMZZ](/sequence-files/IGVFFI9898PMZZ/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI7124VTBR](/sequence-files/IGVFFI7124VTBR/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) has a sequence file [IGVFFI1864UPQB](/sequence-files/IGVFFI1864UPQB/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) 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/IGVFDS9698PDND/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS9698PDND](/measurement-sets/IGVFDS9698PDND/) 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/IGVFDS9698PDND/"
            }
        ]
    },
    "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": "2024-02-12T21:12:45.928723+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2457AMDL/",
            "accession": "IGVFDO2457AMDL",
            "aliases": [
                "bradley-bernstein:Donor 1509",
                "buenrostro-bernstein:Donor 1509"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI1766EGWZ/",
            "accession": "IGVFFI1766EGWZ",
            "aliases": [
                "bradley-bernstein:SS-LS_1620_R2",
                "buenrostro-bernstein:SS-LS_1620_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:31:59.358683+00:00",
            "file_format": "fastq",
            "file_size": 2210768164,
            "href": "/sequence-files/IGVFFI1766EGWZ/@@download/IGVFFI1766EGWZ.fastq.gz",
            "md5sum": "6af10ee3432542cacdadace08054bae2",
            "s3_uri": "s3://igvf-files/2024/02/12/e692bbd6-1fcd-4f76-9ad6-df18179f5dd3/IGVFFI1766EGWZ.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-1117_L3_SS-PKR-5_SS-V1-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1914CZDQ/",
            "accession": "IGVFFI1914CZDQ",
            "aliases": [
                "bradley-bernstein:SS-LS_1716_R2",
                "buenrostro-bernstein:SS-LS_1716_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:33:00.612951+00:00",
            "file_format": "fastq",
            "file_size": 2240677973,
            "href": "/sequence-files/IGVFFI1914CZDQ/@@download/IGVFFI1914CZDQ.fastq.gz",
            "md5sum": "3385c8dde730afd728717e8b4baae95d",
            "s3_uri": "s3://igvf-files/2024/02/12/ab143298-dbda-4ef0-9cc5-13c02fce6e4f/IGVFFI1914CZDQ.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-1117_L4_SS-PKR-5_SS-V1-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7105ZLWV/",
            "accession": "IGVFFI7105ZLWV",
            "aliases": [
                "bradley-bernstein:SS-LS_1620_R1",
                "buenrostro-bernstein:SS-LS_1620_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:31:58.492396+00:00",
            "file_format": "fastq",
            "file_size": 824062059,
            "href": "/sequence-files/IGVFFI7105ZLWV/@@download/IGVFFI7105ZLWV.fastq.gz",
            "md5sum": "59c3ad855f017e4643f3dab870b9c949",
            "s3_uri": "s3://igvf-files/2024/02/12/513df970-1d33-4614-bd14-f41b6db9b4a7/IGVFFI7105ZLWV.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-1117_L3_SS-PKR-5_SS-V1-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0445CBFR/",
            "accession": "IGVFFI0445CBFR",
            "aliases": [
                "bradley-bernstein:SS-LS_1428_R1",
                "buenrostro-bernstein:SS-LS_1428_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:30:44.166995+00:00",
            "file_format": "fastq",
            "file_size": 833480430,
            "href": "/sequence-files/IGVFFI0445CBFR/@@download/IGVFFI0445CBFR.fastq.gz",
            "md5sum": "acbda85aa14d5d4556336e3fcd05632a",
            "s3_uri": "s3://igvf-files/2024/02/12/05ad248f-9a9d-46c1-bd7d-28bb3d530ea9/IGVFFI0445CBFR.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-1117_L1_SS-PKR-5_SS-V1-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2985KCGA/",
            "accession": "IGVFFI2985KCGA",
            "aliases": [
                "bradley-bernstein:SS-LS_1428_R2",
                "buenrostro-bernstein:SS-LS_1428_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:30:45.171416+00:00",
            "file_format": "fastq",
            "file_size": 2228957724,
            "href": "/sequence-files/IGVFFI2985KCGA/@@download/IGVFFI2985KCGA.fastq.gz",
            "md5sum": "9f925ead52cd0bfd8ab99a3999ed7419",
            "s3_uri": "s3://igvf-files/2024/02/12/f1c7256f-746d-477b-9cf6-a85a34872f52/IGVFFI2985KCGA.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-1117_L1_SS-PKR-5_SS-V1-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2001SFNQ/",
            "accession": "IGVFFI2001SFNQ",
            "aliases": [
                "bradley-bernstein:SS-LS_1524_R1",
                "buenrostro-bernstein:SS-LS_1524_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:31:23.448206+00:00",
            "file_format": "fastq",
            "file_size": 850302637,
            "href": "/sequence-files/IGVFFI2001SFNQ/@@download/IGVFFI2001SFNQ.fastq.gz",
            "md5sum": "da0fc68320c6254e1ac12d8e96131bdb",
            "s3_uri": "s3://igvf-files/2024/02/12/912dd4bb-c2c9-4adc-b73c-a43e5ed3c502/IGVFFI2001SFNQ.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-1117_L2_SS-PKR-5_SS-V1-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8332UVED/",
            "accession": "IGVFFI8332UVED",
            "aliases": [
                "bradley-bernstein:SS-LS_1716_R1",
                "buenrostro-bernstein:SS-LS_1716_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:32:59.608679+00:00",
            "file_format": "fastq",
            "file_size": 824204748,
            "href": "/sequence-files/IGVFFI8332UVED/@@download/IGVFFI8332UVED.fastq.gz",
            "md5sum": "d26b5d9ccb06bad0ed09e25349122c7d",
            "s3_uri": "s3://igvf-files/2024/02/12/d74e887e-3755-480f-9443-dfd1ba4c26fa/IGVFFI8332UVED.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-1117_L4_SS-PKR-5_SS-V1-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1009RQOH/",
            "accession": "IGVFFI1009RQOH",
            "aliases": [
                "bradley-bernstein:SS-LS_2386_R2",
                "buenrostro-bernstein:SS-LS_2386_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:34:17.220646+00:00",
            "file_format": "fastq",
            "file_size": 1045470209,
            "href": "/sequence-files/IGVFFI1009RQOH/@@download/IGVFFI1009RQOH.fastq.gz",
            "md5sum": "bd410654057d5715367d0913622fea8a",
            "s3_uri": "s3://igvf-files/2024/02/12/ee8adc94-e3bf-49ca-9428-37edb8b7b7ca/IGVFFI1009RQOH.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-54_L2_SS-PKR-5_SS-V1-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9434DEGG/",
            "accession": "IGVFFI9434DEGG",
            "aliases": [
                "bradley-bernstein:SS-LS_2482_R2",
                "buenrostro-bernstein:SS-LS_2482_R2"
            ],
            "content_type": "reads",
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