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IGVFDS2528FCFL

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2528FCFL/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2528FCFL",
    "aliases": [
        "bradley-bernstein:scRNA Lib 14",
        "buenrostro-bernstein:scRNA Lib 14"
    ],
    "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 [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "mismatched status",
                "detail": "Released primary cell [IGVFSM7081AOVO](/primary-cells/IGVFSM7081AOVO/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM7081AOVO/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM7081AOVO](/primary-cells/IGVFSM7081AOVO/) 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/IGVFSM7081AOVO/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has sequence file(s): [IGVFFI7309KTUY](/sequence-files/IGVFFI7309KTUY/), [IGVFFI7491AOOQ](/sequence-files/IGVFFI7491AOOQ/), [IGVFFI9517YYRK](/sequence-files/IGVFFI9517YYRK/), [IGVFFI2094OYTN](/sequence-files/IGVFFI2094OYTN/), [IGVFFI2608JTQS](/sequence-files/IGVFFI2608JTQS/), [IGVFFI7401KOEF](/sequence-files/IGVFFI7401KOEF/), [IGVFFI8711UGMS](/sequence-files/IGVFFI8711UGMS/), [IGVFFI9144TIHN](/sequence-files/IGVFFI9144TIHN/), [IGVFFI6080ZOFN](/sequence-files/IGVFFI6080ZOFN/), [IGVFFI7929CQMB](/sequence-files/IGVFFI7929CQMB/), [IGVFFI4202HURV](/sequence-files/IGVFFI4202HURV/), [IGVFFI6440FNEC](/sequence-files/IGVFFI6440FNEC/), [IGVFFI9684MRVS](/sequence-files/IGVFFI9684MRVS/), [IGVFFI8545QHXH](/sequence-files/IGVFFI8545QHXH/), [IGVFFI2795GMDA](/sequence-files/IGVFFI2795GMDA/), [IGVFFI5233SIJB](/sequence-files/IGVFFI5233SIJB/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI7309KTUY](/sequence-files/IGVFFI7309KTUY/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI7491AOOQ](/sequence-files/IGVFFI7491AOOQ/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI9517YYRK](/sequence-files/IGVFFI9517YYRK/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI2094OYTN](/sequence-files/IGVFFI2094OYTN/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI2608JTQS](/sequence-files/IGVFFI2608JTQS/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI7401KOEF](/sequence-files/IGVFFI7401KOEF/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI8711UGMS](/sequence-files/IGVFFI8711UGMS/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI9144TIHN](/sequence-files/IGVFFI9144TIHN/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI6080ZOFN](/sequence-files/IGVFFI6080ZOFN/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI7929CQMB](/sequence-files/IGVFFI7929CQMB/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI4202HURV](/sequence-files/IGVFFI4202HURV/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI6440FNEC](/sequence-files/IGVFFI6440FNEC/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI9684MRVS](/sequence-files/IGVFFI9684MRVS/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI8545QHXH](/sequence-files/IGVFFI8545QHXH/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI2795GMDA](/sequence-files/IGVFFI2795GMDA/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) has a sequence file [IGVFFI5233SIJB](/sequence-files/IGVFFI5233SIJB/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) 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/IGVFDS2528FCFL/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS2528FCFL](/measurement-sets/IGVFDS2528FCFL/) 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/IGVFDS2528FCFL/"
            }
        ]
    },
    "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": "2024-02-12T21:12:32.987374+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2605CUSL/",
            "accession": "IGVFDO2605CUSL",
            "aliases": [
                "bradley-bernstein:Donor 1508",
                "buenrostro-bernstein:Donor 1508"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI7309KTUY/",
            "accession": "IGVFFI7309KTUY",
            "aliases": [
                "bradley-bernstein:SS-LS_1594_R1",
                "buenrostro-bernstein:SS-LS_1594_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:26:34.441168+00:00",
            "file_format": "fastq",
            "file_size": 1205079428,
            "href": "/sequence-files/IGVFFI7309KTUY/@@download/IGVFFI7309KTUY.fastq.gz",
            "md5sum": "b6ed07861b575b6de5fb50d9d2ace01b",
            "s3_uri": "s3://igvf-files/2024/02/12/3474701a-a020-4316-84c7-5c390db361cb/IGVFFI7309KTUY.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-1091_L3_SS-PKR-3_SS-V1-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7491AOOQ/",
            "accession": "IGVFFI7491AOOQ",
            "aliases": [
                "bradley-bernstein:SS-LS_1690_R2",
                "buenrostro-bernstein:SS-LS_1690_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:27:11.673406+00:00",
            "file_format": "fastq",
            "file_size": 2876402792,
            "href": "/sequence-files/IGVFFI7491AOOQ/@@download/IGVFFI7491AOOQ.fastq.gz",
            "md5sum": "10e59697a6e168409c09862240cd4ad8",
            "s3_uri": "s3://igvf-files/2024/02/12/014dda78-353a-4712-ab5c-420d8735de2f/IGVFFI7491AOOQ.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-1091_L4_SS-PKR-3_SS-V1-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9517YYRK/",
            "accession": "IGVFFI9517YYRK",
            "aliases": [
                "bradley-bernstein:SS-LS_1402_R1",
                "buenrostro-bernstein:SS-LS_1402_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:25:21.825196+00:00",
            "file_format": "fastq",
            "file_size": 1208470495,
            "href": "/sequence-files/IGVFFI9517YYRK/@@download/IGVFFI9517YYRK.fastq.gz",
            "md5sum": "b624849d2a25d56ec4bf26944fdcc4b9",
            "s3_uri": "s3://igvf-files/2024/02/12/49c4ef1e-80d8-469f-abdd-00b8fb241091/IGVFFI9517YYRK.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-1091_L1_SS-PKR-3_SS-V1-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2094OYTN/",
            "accession": "IGVFFI2094OYTN",
            "aliases": [
                "bradley-bernstein:SS-LS_1498_R1",
                "buenrostro-bernstein:SS-LS_1498_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:25:56.404345+00:00",
            "file_format": "fastq",
            "file_size": 1222754047,
            "href": "/sequence-files/IGVFFI2094OYTN/@@download/IGVFFI2094OYTN.fastq.gz",
            "md5sum": "19ace2c8c55e03a7466c674e62ede758",
            "s3_uri": "s3://igvf-files/2024/02/12/14f11e0a-49a5-4408-bf2b-03624e6ba22f/IGVFFI2094OYTN.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-1091_L2_SS-PKR-3_SS-V1-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2608JTQS/",
            "accession": "IGVFFI2608JTQS",
            "aliases": [
                "bradley-bernstein:SS-LS_1690_R1",
                "buenrostro-bernstein:SS-LS_1690_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:27:10.636664+00:00",
            "file_format": "fastq",
            "file_size": 1225976381,
            "href": "/sequence-files/IGVFFI2608JTQS/@@download/IGVFFI2608JTQS.fastq.gz",
            "md5sum": "8ce5bb2418698441d4154fee3b88e695",
            "s3_uri": "s3://igvf-files/2024/02/12/f9339a1d-bb32-4166-a163-aeaa4a9eccac/IGVFFI2608JTQS.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-1091_L4_SS-PKR-3_SS-V1-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7401KOEF/",
            "accession": "IGVFFI7401KOEF",
            "aliases": [
                "bradley-bernstein:SS-LS_2360_R2",
                "buenrostro-bernstein:SS-LS_2360_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:28:46.379212+00:00",
            "file_format": "fastq",
            "file_size": 1006270053,
            "href": "/sequence-files/IGVFFI7401KOEF/@@download/IGVFFI7401KOEF.fastq.gz",
            "md5sum": "3f6d65c7d3cc5057b8a7d41e5e060c08",
            "s3_uri": "s3://igvf-files/2024/02/12/c232507a-ba45-49a9-867e-a396d5f882c4/IGVFFI7401KOEF.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-28_L2_SS-PKR-3_SS-V1-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8711UGMS/",
            "accession": "IGVFFI8711UGMS",
            "aliases": [
                "bradley-bernstein:SS-LS_2264_R2",
                "buenrostro-bernstein:SS-LS_2264_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:27:46.761634+00:00",
            "file_format": "fastq",
            "file_size": 1005098523,
            "href": "/sequence-files/IGVFFI8711UGMS/@@download/IGVFFI8711UGMS.fastq.gz",
            "md5sum": "1c79757ffeda2821106aa1f49f3f7eef",
            "s3_uri": "s3://igvf-files/2024/02/12/76792b22-af0d-4481-be95-7b7e8150ab81/IGVFFI8711UGMS.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-28_L1_SS-PKR-3_SS-V1-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9144TIHN/",
            "accession": "IGVFFI9144TIHN",
            "aliases": [
                "bradley-bernstein:SS-LS_1402_R2",
                "buenrostro-bernstein:SS-LS_1402_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:25:22.781898+00:00",
            "file_format": "fastq",
            "file_size": 2833139865,
            "href": "/sequence-files/IGVFFI9144TIHN/@@download/IGVFFI9144TIHN.fastq.gz",
            "md5sum": "ad86d4bd7099d541bd67fe19ce4b0d00",
            "s3_uri": "s3://igvf-files/2024/02/12/0bbe88bf-fcbe-442b-9afe-0c4c23b03b6b/IGVFFI9144TIHN.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-1091_L1_SS-PKR-3_SS-V1-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6080ZOFN/",
            "accession": "IGVFFI6080ZOFN",
            "aliases": [
                "bradley-bernstein:SS-LS_1498_R2",
                "buenrostro-bernstein:SS-LS_1498_R2"
            ],
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