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IGVFDS5892YXLI

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5892YXLI/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5892YXLI",
    "aliases": [
        "bradley-bernstein:scATAC Lib 18",
        "buenrostro-bernstein:scATAC Lib 18"
    ],
    "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 [IGVFSM8105KQWG](/primary-cells/IGVFSM8105KQWG/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/primary-cells/IGVFSM8105KQWG/"
            },
            {
                "category": "missing publication",
                "detail": "Primary cell [IGVFSM8105KQWG](/primary-cells/IGVFSM8105KQWG/) 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/IGVFSM8105KQWG/"
            },
            {
                "category": "missing publication",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) 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/IGVFDS5892YXLI/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has sequence file(s): [IGVFFI3682BVWW](/sequence-files/IGVFFI3682BVWW/), [IGVFFI6922FZJB](/sequence-files/IGVFFI6922FZJB/), [IGVFFI6454ILRW](/sequence-files/IGVFFI6454ILRW/), [IGVFFI4096OHIE](/sequence-files/IGVFFI4096OHIE/), [IGVFFI2551KLBL](/sequence-files/IGVFFI2551KLBL/), [IGVFFI5072XYMA](/sequence-files/IGVFFI5072XYMA/), [IGVFFI3202KUUI](/sequence-files/IGVFFI3202KUUI/), [IGVFFI9350GIEO](/sequence-files/IGVFFI9350GIEO/), [IGVFFI0583ZODU](/sequence-files/IGVFFI0583ZODU/), [IGVFFI0397JEZE](/sequence-files/IGVFFI0397JEZE/), [IGVFFI0982DOQR](/sequence-files/IGVFFI0982DOQR/), [IGVFFI6154VYJD](/sequence-files/IGVFFI6154VYJD/), [IGVFFI4900OTRO](/sequence-files/IGVFFI4900OTRO/), [IGVFFI6533AWYK](/sequence-files/IGVFFI6533AWYK/), [IGVFFI9460ABCN](/sequence-files/IGVFFI9460ABCN/), [IGVFFI3631FUWX](/sequence-files/IGVFFI3631FUWX/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI3682BVWW](/sequence-files/IGVFFI3682BVWW/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI6922FZJB](/sequence-files/IGVFFI6922FZJB/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI6454ILRW](/sequence-files/IGVFFI6454ILRW/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI4096OHIE](/sequence-files/IGVFFI4096OHIE/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI2551KLBL](/sequence-files/IGVFFI2551KLBL/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI5072XYMA](/sequence-files/IGVFFI5072XYMA/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI3202KUUI](/sequence-files/IGVFFI3202KUUI/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI9350GIEO](/sequence-files/IGVFFI9350GIEO/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI0583ZODU](/sequence-files/IGVFFI0583ZODU/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI0397JEZE](/sequence-files/IGVFFI0397JEZE/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI0982DOQR](/sequence-files/IGVFFI0982DOQR/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI6154VYJD](/sequence-files/IGVFFI6154VYJD/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI4900OTRO](/sequence-files/IGVFFI4900OTRO/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI6533AWYK](/sequence-files/IGVFFI6533AWYK/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI9460ABCN](/sequence-files/IGVFFI9460ABCN/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing read names",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) has a sequence file [IGVFFI3631FUWX](/sequence-files/IGVFFI3631FUWX/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing strand specificity",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) 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/IGVFDS5892YXLI/"
            },
            {
                "category": "missing barcode onlist",
                "detail": "Measurement set [IGVFDS5892YXLI](/measurement-sets/IGVFDS5892YXLI/) 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/IGVFDS5892YXLI/"
            }
        ]
    },
    "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": "2024-02-12T21:13:13.828188+00:00",
    "data_use_limitation_summaries": [
        "No limitations"
    ],
    "donors": [
        {
            "@id": "/human-donors/IGVFDO8099ZPMK/",
            "accession": "IGVFDO8099ZPMK",
            "aliases": [
                "bradley-bernstein:Donor 1507",
                "buenrostro-bernstein:Donor 1507"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3682BVWW/",
            "accession": "IGVFFI3682BVWW",
            "aliases": [
                "bradley-bernstein:SS-LS_1601_R2",
                "buenrostro-bernstein:SS-LS_1601_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:48:24.914092+00:00",
            "file_format": "fastq",
            "file_size": 4124,
            "href": "/sequence-files/IGVFFI3682BVWW/@@download/IGVFFI3682BVWW.fastq.gz",
            "md5sum": "b5b530028c5fbdb7eb4f4d2f796c4a39",
            "s3_uri": "s3://igvf-files/2024/02/12/5630eca2-cb2d-46a5-9a12-e20e89d78111/IGVFFI3682BVWW.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-1098_L3_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6922FZJB/",
            "accession": "IGVFFI6922FZJB",
            "aliases": [
                "bradley-bernstein:SS-LS_1505_R1",
                "buenrostro-bernstein:SS-LS_1505_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:47:48.017079+00:00",
            "file_format": "fastq",
            "file_size": 1934,
            "href": "/sequence-files/IGVFFI6922FZJB/@@download/IGVFFI6922FZJB.fastq.gz",
            "md5sum": "110a38f33013e08231bdb053e9468f29",
            "s3_uri": "s3://igvf-files/2024/02/12/dfee981b-ac0f-43c6-87c7-aed741f05526/IGVFFI6922FZJB.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-1098_L2_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6454ILRW/",
            "accession": "IGVFFI6454ILRW",
            "aliases": [
                "bradley-bernstein:SS-LS_2271_R1",
                "buenrostro-bernstein:SS-LS_2271_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:50:05.738936+00:00",
            "file_format": "fastq",
            "file_size": 505323233,
            "href": "/sequence-files/IGVFFI6454ILRW/@@download/IGVFFI6454ILRW.fastq.gz",
            "md5sum": "cef0f16573134b7f7a41823bf96f7a2b",
            "s3_uri": "s3://igvf-files/2024/02/12/1e678ffb-b65c-4ed4-8295-b8d4dcc43af0/IGVFFI6454ILRW.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-35_L1_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4096OHIE/",
            "accession": "IGVFFI4096OHIE",
            "aliases": [
                "bradley-bernstein:SS-LS_2559_R1",
                "buenrostro-bernstein:SS-LS_2559_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:52:02.080484+00:00",
            "file_format": "fastq",
            "file_size": 502190372,
            "href": "/sequence-files/IGVFFI4096OHIE/@@download/IGVFFI4096OHIE.fastq.gz",
            "md5sum": "bf3d9c9e7544aa00fd0a0aafe2e4c77e",
            "s3_uri": "s3://igvf-files/2024/02/12/2ab604cc-a342-4394-9435-0f9025333ab0/IGVFFI4096OHIE.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-35_L4_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2551KLBL/",
            "accession": "IGVFFI2551KLBL",
            "aliases": [
                "bradley-bernstein:SS-LS_2271_R2",
                "buenrostro-bernstein:SS-LS_2271_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:50:06.675872+00:00",
            "file_format": "fastq",
            "file_size": 871439153,
            "href": "/sequence-files/IGVFFI2551KLBL/@@download/IGVFFI2551KLBL.fastq.gz",
            "md5sum": "4895ff3435f8b422f0301e3175778efb",
            "s3_uri": "s3://igvf-files/2024/02/12/19e59571-9137-43ab-ae77-f253abe8666e/IGVFFI2551KLBL.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-35_L1_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5072XYMA/",
            "accession": "IGVFFI5072XYMA",
            "aliases": [
                "bradley-bernstein:SS-LS_1505_R2",
                "buenrostro-bernstein:SS-LS_1505_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:47:49.122753+00:00",
            "file_format": "fastq",
            "file_size": 3238,
            "href": "/sequence-files/IGVFFI5072XYMA/@@download/IGVFFI5072XYMA.fastq.gz",
            "md5sum": "a87fcfd103e317277fafe630349eae90",
            "s3_uri": "s3://igvf-files/2024/02/12/772a1ce2-e74c-4465-b2c0-bb49b65b0919/IGVFFI5072XYMA.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-1098_L2_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3202KUUI/",
            "accession": "IGVFFI3202KUUI",
            "aliases": [
                "bradley-bernstein:SS-LS_1697_R1",
                "buenrostro-bernstein:SS-LS_1697_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:49:07.006296+00:00",
            "file_format": "fastq",
            "file_size": 2014,
            "href": "/sequence-files/IGVFFI3202KUUI/@@download/IGVFFI3202KUUI.fastq.gz",
            "md5sum": "30a87ca64ffd8cafd312de84aa3a8a8e",
            "s3_uri": "s3://igvf-files/2024/02/12/e327bbb0-fa64-4f06-a31c-bf6e86efca8e/IGVFFI3202KUUI.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-1098_L4_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9350GIEO/",
            "accession": "IGVFFI9350GIEO",
            "aliases": [
                "bradley-bernstein:SS-LS_1697_R2",
                "buenrostro-bernstein:SS-LS_1697_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-12T21:49:07.901954+00:00",
            "file_format": "fastq",
            "file_size": 3461,
            "href": "/sequence-files/IGVFFI9350GIEO/@@download/IGVFFI9350GIEO.fastq.gz",
            "md5sum": "661cd70ff9a92ae8fbd68c985bcaa70b",
            "s3_uri": "s3://igvf-files/2024/02/12/aecb7044-9f1b-4ca3-aaae-9ba50866bd0f/IGVFFI9350GIEO.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-1098_L4_SS-PKR-3_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0583ZODU/",
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