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IGVFDS2636NOED

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2636NOED/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2636NOED",
    "aliases": [
        "bradley-bernstein:scATAC Lib 41",
        "buenrostro-bernstein:scATAC Lib 41"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002764/",
        "assay_slims": [
            "chromatin accessibility"
        ],
        "status": "released",
        "term_name": "single-cell ATAC-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "mismatched status",
                "detail": "Released primary cell [IGVFSM8077ATDC](/primary-cells/IGVFSM8077ATDC/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM8077ATDC/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM8077ATDC](/primary-cells/IGVFSM8077ATDC/) 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/IGVFSM8077ATDC/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has sequence file(s): [IGVFFI3152LJJF](/sequence-files/IGVFFI3152LJJF/), [IGVFFI6794XSOX](/sequence-files/IGVFFI6794XSOX/), [IGVFFI0890PVCX](/sequence-files/IGVFFI0890PVCX/), [IGVFFI9876AHYR](/sequence-files/IGVFFI9876AHYR/), [IGVFFI9687EHCD](/sequence-files/IGVFFI9687EHCD/), [IGVFFI8601HBGN](/sequence-files/IGVFFI8601HBGN/), [IGVFFI5484OLNU](/sequence-files/IGVFFI5484OLNU/), [IGVFFI1631KYED](/sequence-files/IGVFFI1631KYED/), [IGVFFI7218AYRN](/sequence-files/IGVFFI7218AYRN/), [IGVFFI9122WYFN](/sequence-files/IGVFFI9122WYFN/), [IGVFFI1648WAMC](/sequence-files/IGVFFI1648WAMC/), [IGVFFI2999CITH](/sequence-files/IGVFFI2999CITH/), [IGVFFI3800EMMD](/sequence-files/IGVFFI3800EMMD/), [IGVFFI9056AVVY](/sequence-files/IGVFFI9056AVVY/), [IGVFFI3103ATIU](/sequence-files/IGVFFI3103ATIU/), [IGVFFI2406BTJV](/sequence-files/IGVFFI2406BTJV/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI3152LJJF](/sequence-files/IGVFFI3152LJJF/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI6794XSOX](/sequence-files/IGVFFI6794XSOX/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI0890PVCX](/sequence-files/IGVFFI0890PVCX/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI9876AHYR](/sequence-files/IGVFFI9876AHYR/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI9687EHCD](/sequence-files/IGVFFI9687EHCD/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI8601HBGN](/sequence-files/IGVFFI8601HBGN/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI5484OLNU](/sequence-files/IGVFFI5484OLNU/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI1631KYED](/sequence-files/IGVFFI1631KYED/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI7218AYRN](/sequence-files/IGVFFI7218AYRN/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI9122WYFN](/sequence-files/IGVFFI9122WYFN/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI1648WAMC](/sequence-files/IGVFFI1648WAMC/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI2999CITH](/sequence-files/IGVFFI2999CITH/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI3800EMMD](/sequence-files/IGVFFI3800EMMD/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI9056AVVY](/sequence-files/IGVFFI9056AVVY/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI3103ATIU](/sequence-files/IGVFFI3103ATIU/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has a sequence file [IGVFFI2406BTJV](/sequence-files/IGVFFI2406BTJV/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) 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/IGVFDS2636NOED/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS2636NOED](/measurement-sets/IGVFDS2636NOED/) has an `assay_term` of single-cell ATAC-seq 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/IGVFDS2636NOED/"
            }
        ]
    },
    "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": "2024-02-12T21:13:08.909823+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2174SHTA/",
            "accession": "IGVFDO2174SHTA",
            "aliases": [
                "bradley-bernstein:Donor 1510",
                "buenrostro-bernstein:Donor 1510"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3152LJJF/",
            "accession": "IGVFFI3152LJJF",
            "aliases": [
                "bradley-bernstein:SS-LS_1455_R2",
                "buenrostro-bernstein:SS-LS_1455_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:41:54.832175+00:00",
            "file_format": "fastq",
            "file_size": 8347,
            "href": "/sequence-files/IGVFFI3152LJJF/@@download/IGVFFI3152LJJF.fastq.gz",
            "md5sum": "4b9859ad91d5992e36724f922d82409f",
            "s3_uri": "s3://igvf-files/2024/02/12/86de5b75-7d0f-4631-8358-3c825c6377c1/IGVFFI3152LJJF.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-1144_L1_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6794XSOX/",
            "accession": "IGVFFI6794XSOX",
            "aliases": [
                "bradley-bernstein:SS-LS_1551_R2",
                "buenrostro-bernstein:SS-LS_1551_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:42:37.745645+00:00",
            "file_format": "fastq",
            "file_size": 7808,
            "href": "/sequence-files/IGVFFI6794XSOX/@@download/IGVFFI6794XSOX.fastq.gz",
            "md5sum": "80b97f32b023275ef65d83ec63eac75d",
            "s3_uri": "s3://igvf-files/2024/02/12/2ab99036-69b5-4493-8cc6-f3960a9d114f/IGVFFI6794XSOX.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-1144_L2_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0890PVCX/",
            "accession": "IGVFFI0890PVCX",
            "aliases": [
                "bradley-bernstein:SS-LS_1551_R1",
                "buenrostro-bernstein:SS-LS_1551_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:42:36.814225+00:00",
            "file_format": "fastq",
            "file_size": 4001,
            "href": "/sequence-files/IGVFFI0890PVCX/@@download/IGVFFI0890PVCX.fastq.gz",
            "md5sum": "bd15097dc2128b2458d003b3f35c3850",
            "s3_uri": "s3://igvf-files/2024/02/12/ff39106d-812b-47f4-9b60-36c8e38f0b71/IGVFFI0890PVCX.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-1144_L2_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9876AHYR/",
            "accession": "IGVFFI9876AHYR",
            "aliases": [
                "bradley-bernstein:SS-LS_1455_R1",
                "buenrostro-bernstein:SS-LS_1455_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:41:53.901168+00:00",
            "file_format": "fastq",
            "file_size": 4266,
            "href": "/sequence-files/IGVFFI9876AHYR/@@download/IGVFFI9876AHYR.fastq.gz",
            "md5sum": "338157588541e920319d4b9019f79f29",
            "s3_uri": "s3://igvf-files/2024/02/12/9b7f0443-1d57-4548-8284-80138f713cc1/IGVFFI9876AHYR.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-1144_L1_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9687EHCD/",
            "accession": "IGVFFI9687EHCD",
            "aliases": [
                "bradley-bernstein:SS-LS_1647_R1",
                "buenrostro-bernstein:SS-LS_1647_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:43:11.666894+00:00",
            "file_format": "fastq",
            "file_size": 3769,
            "href": "/sequence-files/IGVFFI9687EHCD/@@download/IGVFFI9687EHCD.fastq.gz",
            "md5sum": "24f3b6c46a75e695bd515b6ef7ae1a45",
            "s3_uri": "s3://igvf-files/2024/02/12/1d4008b6-c07f-457a-8023-4e6f098197ed/IGVFFI9687EHCD.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-1144_L3_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8601HBGN/",
            "accession": "IGVFFI8601HBGN",
            "aliases": [
                "bradley-bernstein:SS-LS_2317_R1",
                "buenrostro-bernstein:SS-LS_2317_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:44:27.093254+00:00",
            "file_format": "fastq",
            "file_size": 285572970,
            "href": "/sequence-files/IGVFFI8601HBGN/@@download/IGVFFI8601HBGN.fastq.gz",
            "md5sum": "53b18b46ab650e16d9316047ba007843",
            "s3_uri": "s3://igvf-files/2024/02/12/98e31116-0124-49e8-8e44-f67f9eafc440/IGVFFI8601HBGN.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-81_L1_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5484OLNU/",
            "accession": "IGVFFI5484OLNU",
            "aliases": [
                "bradley-bernstein:SS-LS_2605_R2",
                "buenrostro-bernstein:SS-LS_2605_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:46:49.529515+00:00",
            "file_format": "fastq",
            "file_size": 501009949,
            "href": "/sequence-files/IGVFFI5484OLNU/@@download/IGVFFI5484OLNU.fastq.gz",
            "md5sum": "768270f021c7d1776118812d50c476f9",
            "s3_uri": "s3://igvf-files/2024/02/12/39ff3ca4-b98f-4574-891e-9acf976d1181/IGVFFI5484OLNU.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-81_L4_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1631KYED/",
            "accession": "IGVFFI1631KYED",
            "aliases": [
                "bradley-bernstein:SS-LS_2509_R1",
                "buenrostro-bernstein:SS-LS_2509_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:46:11.380394+00:00",
            "file_format": "fastq",
            "file_size": 285792556,
            "href": "/sequence-files/IGVFFI1631KYED/@@download/IGVFFI1631KYED.fastq.gz",
            "md5sum": "5deb086576b90c799017c9fd239fa23b",
            "s3_uri": "s3://igvf-files/2024/02/12/ea20b3b8-3423-47e7-96ef-c2c603da21c8/IGVFFI1631KYED.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-81_L3_SS-PKR-7_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7218AYRN/",
            "accession": "IGVFFI7218AYRN",
            "aliases": [
                "bradley-bernstein:SS-LS_1743_R1",
                "buenrostro-bernstein:SS-LS_1743_R1"
            ],
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