{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2451WVVC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2451WVVC",
"aliases": [
"bradley-bernstein:scATAC Lib 11",
"buenrostro-bernstein:scATAC Lib 11"
],
"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 [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) 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/IGVFDS2451WVVC/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM6909NWSZ](/primary-cells/IGVFSM6909NWSZ/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM6909NWSZ/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM6909NWSZ](/primary-cells/IGVFSM6909NWSZ/) 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/IGVFSM6909NWSZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has sequence file(s): [IGVFFI6140GLMX](/sequence-files/IGVFFI6140GLMX/), [IGVFFI3138MPIQ](/sequence-files/IGVFFI3138MPIQ/), [IGVFFI9632MVNQ](/sequence-files/IGVFFI9632MVNQ/), [IGVFFI3815ENHO](/sequence-files/IGVFFI3815ENHO/), [IGVFFI6007KVXA](/sequence-files/IGVFFI6007KVXA/), [IGVFFI4771FRPL](/sequence-files/IGVFFI4771FRPL/), [IGVFFI3237TNAU](/sequence-files/IGVFFI3237TNAU/), [IGVFFI1667CBYV](/sequence-files/IGVFFI1667CBYV/), [IGVFFI9988RMIX](/sequence-files/IGVFFI9988RMIX/), [IGVFFI0753TASH](/sequence-files/IGVFFI0753TASH/), [IGVFFI2717TEHD](/sequence-files/IGVFFI2717TEHD/), [IGVFFI6227MHJN](/sequence-files/IGVFFI6227MHJN/), [IGVFFI7055MRMG](/sequence-files/IGVFFI7055MRMG/), [IGVFFI4430SPNE](/sequence-files/IGVFFI4430SPNE/), [IGVFFI7633OCKQ](/sequence-files/IGVFFI7633OCKQ/), [IGVFFI1382FFYF](/sequence-files/IGVFFI1382FFYF/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI6140GLMX](/sequence-files/IGVFFI6140GLMX/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI3138MPIQ](/sequence-files/IGVFFI3138MPIQ/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI9632MVNQ](/sequence-files/IGVFFI9632MVNQ/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI3815ENHO](/sequence-files/IGVFFI3815ENHO/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI6007KVXA](/sequence-files/IGVFFI6007KVXA/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI4771FRPL](/sequence-files/IGVFFI4771FRPL/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI3237TNAU](/sequence-files/IGVFFI3237TNAU/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI1667CBYV](/sequence-files/IGVFFI1667CBYV/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI9988RMIX](/sequence-files/IGVFFI9988RMIX/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI0753TASH](/sequence-files/IGVFFI0753TASH/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI2717TEHD](/sequence-files/IGVFFI2717TEHD/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI6227MHJN](/sequence-files/IGVFFI6227MHJN/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI7055MRMG](/sequence-files/IGVFFI7055MRMG/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI4430SPNE](/sequence-files/IGVFFI4430SPNE/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI7633OCKQ](/sequence-files/IGVFFI7633OCKQ/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has a sequence file [IGVFFI1382FFYF](/sequence-files/IGVFFI1382FFYF/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) 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/IGVFDS2451WVVC/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) 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/IGVFDS2451WVVC/"
}
]
},
"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": "2024-02-12T21:13:02.003867+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/IGVFFI6140GLMX/",
"accession": "IGVFFI6140GLMX",
"aliases": [
"bradley-bernstein:SS-LS_1491_R2",
"buenrostro-bernstein:SS-LS_1491_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:12.237597+00:00",
"file_format": "fastq",
"file_size": 8875,
"href": "/sequence-files/IGVFFI6140GLMX/@@download/IGVFFI6140GLMX.fastq.gz",
"md5sum": "696deef9591fae9b8d6fd2508e875ec1",
"s3_uri": "s3://igvf-files/2024/02/12/82fefee4-356b-4531-8c39-5a61bc8a9852/IGVFFI6140GLMX.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-1084_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3138MPIQ/",
"accession": "IGVFFI3138MPIQ",
"aliases": [
"bradley-bernstein:SS-LS_1491_R1",
"buenrostro-bernstein:SS-LS_1491_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:11.228535+00:00",
"file_format": "fastq",
"file_size": 5220,
"href": "/sequence-files/IGVFFI3138MPIQ/@@download/IGVFFI3138MPIQ.fastq.gz",
"md5sum": "fbb396ba6272cad05fe06bf4d4f3b261",
"s3_uri": "s3://igvf-files/2024/02/12/8bfe3327-74a2-4ac5-8f57-1be63857b22d/IGVFFI3138MPIQ.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-1084_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9632MVNQ/",
"accession": "IGVFFI9632MVNQ",
"aliases": [
"bradley-bernstein:SS-LS_1587_R2",
"buenrostro-bernstein:SS-LS_1587_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:49.179563+00:00",
"file_format": "fastq",
"file_size": 8318,
"href": "/sequence-files/IGVFFI9632MVNQ/@@download/IGVFFI9632MVNQ.fastq.gz",
"md5sum": "5cf4a51e288b115de39affd88aab18c8",
"s3_uri": "s3://igvf-files/2024/02/12/e16abd22-372f-4c46-93ec-631e271a0642/IGVFFI9632MVNQ.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-1084_L3_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3815ENHO/",
"accession": "IGVFFI3815ENHO",
"aliases": [
"bradley-bernstein:SS-LS_1395_R2",
"buenrostro-bernstein:SS-LS_1395_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:31.783768+00:00",
"file_format": "fastq",
"file_size": 9206,
"href": "/sequence-files/IGVFFI3815ENHO/@@download/IGVFFI3815ENHO.fastq.gz",
"md5sum": "34efeb7b5c7b7010198c59863ea5e6cd",
"s3_uri": "s3://igvf-files/2024/02/12/205dd148-3a2c-4104-b9ab-b28bde2ef2af/IGVFFI3815ENHO.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-1084_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6007KVXA/",
"accession": "IGVFFI6007KVXA",
"aliases": [
"bradley-bernstein:SS-LS_2257_R2",
"buenrostro-bernstein:SS-LS_2257_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:04.065534+00:00",
"file_format": "fastq",
"file_size": 363212022,
"href": "/sequence-files/IGVFFI6007KVXA/@@download/IGVFFI6007KVXA.fastq.gz",
"md5sum": "39a74f0f64438ad82bbcd9b10058624d",
"s3_uri": "s3://igvf-files/2024/02/12/2f448c8b-2881-40c0-b3fe-805852583881/IGVFFI6007KVXA.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-21_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4771FRPL/",
"accession": "IGVFFI4771FRPL",
"aliases": [
"bradley-bernstein:SS-LS_1395_R1",
"buenrostro-bernstein:SS-LS_1395_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:30.869294+00:00",
"file_format": "fastq",
"file_size": 5344,
"href": "/sequence-files/IGVFFI4771FRPL/@@download/IGVFFI4771FRPL.fastq.gz",
"md5sum": "9121394e7a80712ea9c6560b1b35db91",
"s3_uri": "s3://igvf-files/2024/02/12/ee73e425-dfe3-46ba-a49f-3e3dfce3623e/IGVFFI4771FRPL.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-1084_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3237TNAU/",
"accession": "IGVFFI3237TNAU",
"aliases": [
"bradley-bernstein:SS-LS_1587_R1",
"buenrostro-bernstein:SS-LS_1587_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:48.280399+00:00",
"file_format": "fastq",
"file_size": 4908,
"href": "/sequence-files/IGVFFI3237TNAU/@@download/IGVFFI3237TNAU.fastq.gz",
"md5sum": "f973bb0ab68c7f372279382dd6f14136",
"s3_uri": "s3://igvf-files/2024/02/12/a4bc718c-536c-44e4-8f3c-f849b75616bb/IGVFFI3237TNAU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1084_L3_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1667CBYV/",
"accession": "IGVFFI1667CBYV",
"aliases": [
"bradley-bernstein:SS-LS_2353_R1",
"buenrostro-bernstein:SS-LS_2353_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:41.169590+00:00",
"file_format": "fastq",
"file_size": 213747590,
"href": "/sequence-files/IGVFFI1667CBYV/@@download/IGVFFI1667CBYV.fastq.gz",
"md5sum": "c7782562037c4796e953dad1aa505c3b",
"s3_uri": "s3://igvf-files/2024/02/12/cd4baa55-bcce-4f8e-9654-6b05febc08d7/IGVFFI1667CBYV.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-21_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9988RMIX/",
"accession": "IGVFFI9988RMIX",
"aliases": [
"bradley-bernstein:SS-LS_2353_R2",
"buenrostro-bernstein:SS-LS_2353_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:42.156726+00:00",
"file_format": "fastq",
"file_size": 364826132,
"href": "/sequence-files/IGVFFI9988RMIX/@@download/IGVFFI9988RMIX.fastq.gz",
"md5sum": "3061c60ee32d0c69425fa0aadb0444a9",
"s3_uri": "s3://igvf-files/2024/02/12/38b8ae0f-fe5e-40d5-b04c-75a9bb9b38c3/IGVFFI9988RMIX.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-21_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0753TASH/",
"accession": "IGVFFI0753TASH",
"aliases": [
"bradley-bernstein:SS-LS_1683_R1",
"buenrostro-bernstein:SS-LS_1683_R1"
],
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