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IGVFDS7919DUHD

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7919DUHD/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7919DUHD",
    "aliases": [
        "bradley-bernstein:scRNA Lib 13",
        "buenrostro-bernstein:scRNA Lib 13"
    ],
    "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 [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "mismatched status",
                "detail": "Released primary cell [IGVFSM6852UYUG](/primary-cells/IGVFSM6852UYUG/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM6852UYUG/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM6852UYUG](/primary-cells/IGVFSM6852UYUG/) 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/IGVFSM6852UYUG/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has sequence file(s): [IGVFFI8559MYDX](/sequence-files/IGVFFI8559MYDX/), [IGVFFI2607LDNU](/sequence-files/IGVFFI2607LDNU/), [IGVFFI2380ARLU](/sequence-files/IGVFFI2380ARLU/), [IGVFFI9181PQVD](/sequence-files/IGVFFI9181PQVD/), [IGVFFI1693EDXK](/sequence-files/IGVFFI1693EDXK/), [IGVFFI7002LZLR](/sequence-files/IGVFFI7002LZLR/), [IGVFFI0178IHNS](/sequence-files/IGVFFI0178IHNS/), [IGVFFI7367DSKV](/sequence-files/IGVFFI7367DSKV/), [IGVFFI5800EUPI](/sequence-files/IGVFFI5800EUPI/), [IGVFFI6606GTSF](/sequence-files/IGVFFI6606GTSF/), [IGVFFI3952NJOF](/sequence-files/IGVFFI3952NJOF/), [IGVFFI4789ZNLM](/sequence-files/IGVFFI4789ZNLM/), [IGVFFI2070DCTH](/sequence-files/IGVFFI2070DCTH/), [IGVFFI8915MCXV](/sequence-files/IGVFFI8915MCXV/), [IGVFFI2536WZTV](/sequence-files/IGVFFI2536WZTV/), [IGVFFI2703DMIN](/sequence-files/IGVFFI2703DMIN/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI8559MYDX](/sequence-files/IGVFFI8559MYDX/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI2607LDNU](/sequence-files/IGVFFI2607LDNU/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI2380ARLU](/sequence-files/IGVFFI2380ARLU/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI9181PQVD](/sequence-files/IGVFFI9181PQVD/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI1693EDXK](/sequence-files/IGVFFI1693EDXK/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI7002LZLR](/sequence-files/IGVFFI7002LZLR/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI0178IHNS](/sequence-files/IGVFFI0178IHNS/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI7367DSKV](/sequence-files/IGVFFI7367DSKV/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI5800EUPI](/sequence-files/IGVFFI5800EUPI/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI6606GTSF](/sequence-files/IGVFFI6606GTSF/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI3952NJOF](/sequence-files/IGVFFI3952NJOF/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI4789ZNLM](/sequence-files/IGVFFI4789ZNLM/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI2070DCTH](/sequence-files/IGVFFI2070DCTH/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI8915MCXV](/sequence-files/IGVFFI8915MCXV/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI2536WZTV](/sequence-files/IGVFFI2536WZTV/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) has a sequence file [IGVFFI2703DMIN](/sequence-files/IGVFFI2703DMIN/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) 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/IGVFDS7919DUHD/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS7919DUHD](/measurement-sets/IGVFDS7919DUHD/) 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/IGVFDS7919DUHD/"
            }
        ]
    },
    "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": "2024-02-12T21:12:23.036574+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/IGVFFI8559MYDX/",
            "accession": "IGVFFI8559MYDX",
            "aliases": [
                "bradley-bernstein:SS-LS_1400_R2",
                "buenrostro-bernstein:SS-LS_1400_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:23:29.312498+00:00",
            "file_format": "fastq",
            "file_size": 3145566707,
            "href": "/sequence-files/IGVFFI8559MYDX/@@download/IGVFFI8559MYDX.fastq.gz",
            "md5sum": "51a833fc180064b2c229c87f82027030",
            "s3_uri": "s3://igvf-files/2024/02/12/5947f5c4-305f-4e21-a983-b3c57de2b64d/IGVFFI8559MYDX.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-1089_L1_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2607LDNU/",
            "accession": "IGVFFI2607LDNU",
            "aliases": [
                "bradley-bernstein:SS-LS_1400_R1",
                "buenrostro-bernstein:SS-LS_1400_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:23:28.183769+00:00",
            "file_format": "fastq",
            "file_size": 1343414201,
            "href": "/sequence-files/IGVFFI2607LDNU/@@download/IGVFFI2607LDNU.fastq.gz",
            "md5sum": "c3fad38caf08201b9eca7bc1f6476ea3",
            "s3_uri": "s3://igvf-files/2024/02/12/baa995de-5381-46c3-9e3f-4960c85a5d1c/IGVFFI2607LDNU.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-1089_L1_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2380ARLU/",
            "accession": "IGVFFI2380ARLU",
            "aliases": [
                "bradley-bernstein:SS-LS_2454_R1",
                "buenrostro-bernstein:SS-LS_2454_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:06.524810+00:00",
            "file_format": "fastq",
            "file_size": 537659134,
            "href": "/sequence-files/IGVFFI2380ARLU/@@download/IGVFFI2380ARLU.fastq.gz",
            "md5sum": "87815e6c638ed215601f8c26e4f26354",
            "s3_uri": "s3://igvf-files/2024/02/12/44a19b40-9f90-4ea6-b712-f3e455cfa90d/IGVFFI2380ARLU.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-26_L3_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9181PQVD/",
            "accession": "IGVFFI9181PQVD",
            "aliases": [
                "bradley-bernstein:SS-LS_2550_R1",
                "buenrostro-bernstein:SS-LS_2550_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:40.787554+00:00",
            "file_format": "fastq",
            "file_size": 527826861,
            "href": "/sequence-files/IGVFFI9181PQVD/@@download/IGVFFI9181PQVD.fastq.gz",
            "md5sum": "139a67c7a372ea526795bb0021d1c890",
            "s3_uri": "s3://igvf-files/2024/02/12/549fdc36-bd7a-410c-aa86-4f64d0ab6bdd/IGVFFI9181PQVD.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-26_L4_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1693EDXK/",
            "accession": "IGVFFI1693EDXK",
            "aliases": [
                "bradley-bernstein:SS-LS_2550_R2",
                "buenrostro-bernstein:SS-LS_2550_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:41.905677+00:00",
            "file_format": "fastq",
            "file_size": 1102796814,
            "href": "/sequence-files/IGVFFI1693EDXK/@@download/IGVFFI1693EDXK.fastq.gz",
            "md5sum": "34f8deb376ccd33f6f85ef0929ed2007",
            "s3_uri": "s3://igvf-files/2024/02/12/664710ab-9a3e-417b-b9d7-d36fc8aa5221/IGVFFI1693EDXK.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-26_L4_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7002LZLR/",
            "accession": "IGVFFI7002LZLR",
            "aliases": [
                "bradley-bernstein:SS-LS_1496_R1",
                "buenrostro-bernstein:SS-LS_1496_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:27:56.258258+00:00",
            "file_format": "fastq",
            "file_size": 1359797558,
            "href": "/sequence-files/IGVFFI7002LZLR/@@download/IGVFFI7002LZLR.fastq.gz",
            "md5sum": "5d0b43ed7712bdc611540459908a354b",
            "s3_uri": "s3://igvf-files/2024/02/12/d4a81588-445a-4720-92af-5ef5e922632b/IGVFFI7002LZLR.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-1089_L2_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0178IHNS/",
            "accession": "IGVFFI0178IHNS",
            "aliases": [
                "bradley-bernstein:SS-LS_2454_R2",
                "buenrostro-bernstein:SS-LS_2454_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:24:07.484805+00:00",
            "file_format": "fastq",
            "file_size": 1118141849,
            "href": "/sequence-files/IGVFFI0178IHNS/@@download/IGVFFI0178IHNS.fastq.gz",
            "md5sum": "7fd5a11a08958e3ce183df696145057c",
            "s3_uri": "s3://igvf-files/2024/02/12/992c1468-c9b5-435b-970e-1e5e45077231/IGVFFI0178IHNS.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-26_L3_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7367DSKV/",
            "accession": "IGVFFI7367DSKV",
            "aliases": [
                "bradley-bernstein:SS-LS_1496_R2",
                "buenrostro-bernstein:SS-LS_1496_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:27:57.272341+00:00",
            "file_format": "fastq",
            "file_size": 3188040741,
            "href": "/sequence-files/IGVFFI7367DSKV/@@download/IGVFFI7367DSKV.fastq.gz",
            "md5sum": "bb2844055da9983e7cf9707e61ef4dfe",
            "s3_uri": "s3://igvf-files/2024/02/12/2722c9f6-cd56-4f4e-b3f4-e86e56d4aa91/IGVFFI7367DSKV.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-1089_L2_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5800EUPI/",
            "accession": "IGVFFI5800EUPI",
            "aliases": [
                "bradley-bernstein:SS-LS_1592_R2",
                "buenrostro-bernstein:SS-LS_1592_R2"
            ],
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