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IGVFDS5266ONOB

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5266ONOB/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5266ONOB",
    "aliases": [
        "bradley-bernstein:scATAC Lib 16",
        "buenrostro-bernstein:scATAC Lib 16"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002764/",
        "assay_slims": [
            "chromatin accessibility"
        ],
        "status": "released",
        "term_name": "single-cell ATAC-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released primary cell [IGVFSM3750ZIQU](/primary-cells/IGVFSM3750ZIQU/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM3750ZIQU/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM3750ZIQU](/primary-cells/IGVFSM3750ZIQU/) 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/IGVFSM3750ZIQU/"
            },
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) 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/IGVFDS5266ONOB/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has sequence file(s): [IGVFFI1088WXYD](/sequence-files/IGVFFI1088WXYD/), [IGVFFI3489NHUK](/sequence-files/IGVFFI3489NHUK/), [IGVFFI8146ULOY](/sequence-files/IGVFFI8146ULOY/), [IGVFFI4453WONR](/sequence-files/IGVFFI4453WONR/), [IGVFFI4273YBDF](/sequence-files/IGVFFI4273YBDF/), [IGVFFI5918GACB](/sequence-files/IGVFFI5918GACB/), [IGVFFI5352VDQK](/sequence-files/IGVFFI5352VDQK/), [IGVFFI2936YIVF](/sequence-files/IGVFFI2936YIVF/), [IGVFFI8228YHSF](/sequence-files/IGVFFI8228YHSF/), [IGVFFI0211HVOS](/sequence-files/IGVFFI0211HVOS/), [IGVFFI7659JIER](/sequence-files/IGVFFI7659JIER/), [IGVFFI3035UARU](/sequence-files/IGVFFI3035UARU/), [IGVFFI1903LLEZ](/sequence-files/IGVFFI1903LLEZ/), [IGVFFI7904KSEE](/sequence-files/IGVFFI7904KSEE/), [IGVFFI2954JGXR](/sequence-files/IGVFFI2954JGXR/), [IGVFFI6790HKPB](/sequence-files/IGVFFI6790HKPB/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI1088WXYD](/sequence-files/IGVFFI1088WXYD/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI3489NHUK](/sequence-files/IGVFFI3489NHUK/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI8146ULOY](/sequence-files/IGVFFI8146ULOY/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI4453WONR](/sequence-files/IGVFFI4453WONR/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI4273YBDF](/sequence-files/IGVFFI4273YBDF/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI5918GACB](/sequence-files/IGVFFI5918GACB/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI5352VDQK](/sequence-files/IGVFFI5352VDQK/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI2936YIVF](/sequence-files/IGVFFI2936YIVF/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI8228YHSF](/sequence-files/IGVFFI8228YHSF/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI0211HVOS](/sequence-files/IGVFFI0211HVOS/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI7659JIER](/sequence-files/IGVFFI7659JIER/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI3035UARU](/sequence-files/IGVFFI3035UARU/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI1903LLEZ](/sequence-files/IGVFFI1903LLEZ/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI7904KSEE](/sequence-files/IGVFFI7904KSEE/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI2954JGXR](/sequence-files/IGVFFI2954JGXR/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has a sequence file [IGVFFI6790HKPB](/sequence-files/IGVFFI6790HKPB/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) 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/IGVFDS5266ONOB/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) 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/IGVFDS5266ONOB/"
            }
        ]
    },
    "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": "2024-02-12T21:12:53.255193+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO8549ATSE/",
            "accession": "IGVFDO8549ATSE",
            "aliases": [
                "bradley-bernstein:Donor 1511",
                "buenrostro-bernstein:Donor 1511"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI1088WXYD/",
            "accession": "IGVFFI1088WXYD",
            "aliases": [
                "bradley-bernstein:SS-LS_1405_R2",
                "buenrostro-bernstein:SS-LS_1405_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:35:54.060358+00:00",
            "file_format": "fastq",
            "file_size": 1575,
            "href": "/sequence-files/IGVFFI1088WXYD/@@download/IGVFFI1088WXYD.fastq.gz",
            "md5sum": "beac29ff100d3a91d83d24fb5767e7c7",
            "s3_uri": "s3://igvf-files/2024/02/12/d4463f17-c0a2-48f6-9ed6-862afc58d991/IGVFFI1088WXYD.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-1094_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3489NHUK/",
            "accession": "IGVFFI3489NHUK",
            "aliases": [
                "bradley-bernstein:SS-LS_1405_R1",
                "buenrostro-bernstein:SS-LS_1405_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:35:53.039765+00:00",
            "file_format": "fastq",
            "file_size": 958,
            "href": "/sequence-files/IGVFFI3489NHUK/@@download/IGVFFI3489NHUK.fastq.gz",
            "md5sum": "08c3f228b8637add156f24b2858f89aa",
            "s3_uri": "s3://igvf-files/2024/02/12/0bea8be4-821e-48c1-9f20-75574b16e530/IGVFFI3489NHUK.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-1094_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8146ULOY/",
            "accession": "IGVFFI8146ULOY",
            "aliases": [
                "bradley-bernstein:SS-LS_1501_R1",
                "buenrostro-bernstein:SS-LS_1501_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:36:55.229626+00:00",
            "file_format": "fastq",
            "file_size": 916,
            "href": "/sequence-files/IGVFFI8146ULOY/@@download/IGVFFI8146ULOY.fastq.gz",
            "md5sum": "d44d4dab2ab0bad20d25ee160980eb6d",
            "s3_uri": "s3://igvf-files/2024/02/12/bdc1bc2e-1d6c-4270-8a82-9d76baf1fb9e/IGVFFI8146ULOY.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-1094_L2_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4453WONR/",
            "accession": "IGVFFI4453WONR",
            "aliases": [
                "bradley-bernstein:SS-LS_1501_R2",
                "buenrostro-bernstein:SS-LS_1501_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:36:56.114321+00:00",
            "file_format": "fastq",
            "file_size": 1521,
            "href": "/sequence-files/IGVFFI4453WONR/@@download/IGVFFI4453WONR.fastq.gz",
            "md5sum": "c034bef02a5105d49b9801ddad9479a5",
            "s3_uri": "s3://igvf-files/2024/02/12/5e5dd7b2-9cab-44a3-84cc-4d65d098a9d4/IGVFFI4453WONR.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-1094_L2_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4273YBDF/",
            "accession": "IGVFFI4273YBDF",
            "aliases": [
                "bradley-bernstein:SS-LS_1693_R2",
                "buenrostro-bernstein:SS-LS_1693_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:38:07.587413+00:00",
            "file_format": "fastq",
            "file_size": 1446,
            "href": "/sequence-files/IGVFFI4273YBDF/@@download/IGVFFI4273YBDF.fastq.gz",
            "md5sum": "445656d71c4e901148a1494cd84afc6e",
            "s3_uri": "s3://igvf-files/2024/02/12/081e8e47-fe92-49cb-8f45-de5bbc99f1bd/IGVFFI4273YBDF.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-1094_L4_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5918GACB/",
            "accession": "IGVFFI5918GACB",
            "aliases": [
                "bradley-bernstein:SS-LS_2267_R2",
                "buenrostro-bernstein:SS-LS_2267_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:38:43.860036+00:00",
            "file_format": "fastq",
            "file_size": 794485541,
            "href": "/sequence-files/IGVFFI5918GACB/@@download/IGVFFI5918GACB.fastq.gz",
            "md5sum": "5bef90ac94d71e7ea45850ccc95c4e07",
            "s3_uri": "s3://igvf-files/2024/02/12/52e76dac-e436-44cb-9b47-0949b8168295/IGVFFI5918GACB.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-31_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5352VDQK/",
            "accession": "IGVFFI5352VDQK",
            "aliases": [
                "bradley-bernstein:SS-LS_1693_R1",
                "buenrostro-bernstein:SS-LS_1693_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:38:06.561959+00:00",
            "file_format": "fastq",
            "file_size": 904,
            "href": "/sequence-files/IGVFFI5352VDQK/@@download/IGVFFI5352VDQK.fastq.gz",
            "md5sum": "9565d74db26dd1c31342f25551a2aa74",
            "s3_uri": "s3://igvf-files/2024/02/12/f2f9bd89-b679-4101-a1d3-80a8ef63bb75/IGVFFI5352VDQK.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-1094_L4_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2936YIVF/",
            "accession": "IGVFFI2936YIVF",
            "aliases": [
                "bradley-bernstein:SS-LS_1597_R1",
                "buenrostro-bernstein:SS-LS_1597_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:37:31.922525+00:00",
            "file_format": "fastq",
            "file_size": 1030,
            "href": "/sequence-files/IGVFFI2936YIVF/@@download/IGVFFI2936YIVF.fastq.gz",
            "md5sum": "3e8d81bc16b90dc88d611c11e6d4364b",
            "s3_uri": "s3://igvf-files/2024/02/12/ef3906cc-fdd3-4ed6-9902-7681ef878456/IGVFFI2936YIVF.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-1094_L3_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8228YHSF/",
            "accession": "IGVFFI8228YHSF",
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