{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5496ZDEU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5496ZDEU",
"aliases": [
"bradley-bernstein:scATAC Lib 29",
"buenrostro-bernstein:scATAC Lib 29"
],
"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 [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) 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/IGVFDS5496ZDEU/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM2899FEKF](/primary-cells/IGVFSM2899FEKF/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2899FEKF/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM2899FEKF](/primary-cells/IGVFSM2899FEKF/) 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/IGVFSM2899FEKF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has sequence file(s): [IGVFFI8771EIYQ](/sequence-files/IGVFFI8771EIYQ/), [IGVFFI6729WIIC](/sequence-files/IGVFFI6729WIIC/), [IGVFFI6538ONEF](/sequence-files/IGVFFI6538ONEF/), [IGVFFI1078BKFZ](/sequence-files/IGVFFI1078BKFZ/), [IGVFFI3921HSNU](/sequence-files/IGVFFI3921HSNU/), [IGVFFI0594JHQL](/sequence-files/IGVFFI0594JHQL/), [IGVFFI1625LMBR](/sequence-files/IGVFFI1625LMBR/), [IGVFFI4128KKPY](/sequence-files/IGVFFI4128KKPY/), [IGVFFI9655XHTW](/sequence-files/IGVFFI9655XHTW/), [IGVFFI4419NRPJ](/sequence-files/IGVFFI4419NRPJ/), [IGVFFI7088TPTS](/sequence-files/IGVFFI7088TPTS/), [IGVFFI6837TZYR](/sequence-files/IGVFFI6837TZYR/), [IGVFFI9021DCKG](/sequence-files/IGVFFI9021DCKG/), [IGVFFI6429FSVZ](/sequence-files/IGVFFI6429FSVZ/), [IGVFFI3624VIXZ](/sequence-files/IGVFFI3624VIXZ/), [IGVFFI4581KNES](/sequence-files/IGVFFI4581KNES/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI8771EIYQ](/sequence-files/IGVFFI8771EIYQ/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI6729WIIC](/sequence-files/IGVFFI6729WIIC/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI6538ONEF](/sequence-files/IGVFFI6538ONEF/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI1078BKFZ](/sequence-files/IGVFFI1078BKFZ/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI3921HSNU](/sequence-files/IGVFFI3921HSNU/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI0594JHQL](/sequence-files/IGVFFI0594JHQL/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI1625LMBR](/sequence-files/IGVFFI1625LMBR/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI4128KKPY](/sequence-files/IGVFFI4128KKPY/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI9655XHTW](/sequence-files/IGVFFI9655XHTW/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI4419NRPJ](/sequence-files/IGVFFI4419NRPJ/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI7088TPTS](/sequence-files/IGVFFI7088TPTS/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI6837TZYR](/sequence-files/IGVFFI6837TZYR/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI9021DCKG](/sequence-files/IGVFFI9021DCKG/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI6429FSVZ](/sequence-files/IGVFFI6429FSVZ/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI3624VIXZ](/sequence-files/IGVFFI3624VIXZ/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) has a sequence file [IGVFFI4581KNES](/sequence-files/IGVFFI4581KNES/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) 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/IGVFDS5496ZDEU/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS5496ZDEU](/measurement-sets/IGVFDS5496ZDEU/) 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/IGVFDS5496ZDEU/"
}
]
},
"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": "2024-02-12T21:13:06.801964+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/IGVFFI8771EIYQ/",
"accession": "IGVFFI8771EIYQ",
"aliases": [
"bradley-bernstein:SS-LS_1431_R2",
"buenrostro-bernstein:SS-LS_1431_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:45.818949+00:00",
"file_format": "fastq",
"file_size": 3417,
"href": "/sequence-files/IGVFFI8771EIYQ/@@download/IGVFFI8771EIYQ.fastq.gz",
"md5sum": "bd2778e14a22d6072f20e627ae665bee",
"s3_uri": "s3://igvf-files/2024/02/12/787a9e01-95b8-4366-b300-64e0c6572c15/IGVFFI8771EIYQ.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-1120_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6729WIIC/",
"accession": "IGVFFI6729WIIC",
"aliases": [
"bradley-bernstein:SS-LS_1623_R1",
"buenrostro-bernstein:SS-LS_1623_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:03.390970+00:00",
"file_format": "fastq",
"file_size": 1979,
"href": "/sequence-files/IGVFFI6729WIIC/@@download/IGVFFI6729WIIC.fastq.gz",
"md5sum": "358e09fa1d35f6e05a01d8043a4eccff",
"s3_uri": "s3://igvf-files/2024/02/12/3c24bee0-503f-46aa-bb10-9d0a84af1835/IGVFFI6729WIIC.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-1120_L3_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6538ONEF/",
"accession": "IGVFFI6538ONEF",
"aliases": [
"bradley-bernstein:SS-LS_1623_R2",
"buenrostro-bernstein:SS-LS_1623_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:04.367640+00:00",
"file_format": "fastq",
"file_size": 3176,
"href": "/sequence-files/IGVFFI6538ONEF/@@download/IGVFFI6538ONEF.fastq.gz",
"md5sum": "6f14757c8e0db2d68468b3d479a6add1",
"s3_uri": "s3://igvf-files/2024/02/12/19d6818b-63a5-4fea-826d-13948253b882/IGVFFI6538ONEF.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-1120_L3_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1078BKFZ/",
"accession": "IGVFFI1078BKFZ",
"aliases": [
"bradley-bernstein:SS-LS_1431_R1",
"buenrostro-bernstein:SS-LS_1431_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:44.750637+00:00",
"file_format": "fastq",
"file_size": 2183,
"href": "/sequence-files/IGVFFI1078BKFZ/@@download/IGVFFI1078BKFZ.fastq.gz",
"md5sum": "262c3fdcde521f501817f6615b9a8957",
"s3_uri": "s3://igvf-files/2024/02/12/77566628-51b6-4096-b082-8ec8db1bfb94/IGVFFI1078BKFZ.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-1120_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3921HSNU/",
"accession": "IGVFFI3921HSNU",
"aliases": [
"bradley-bernstein:SS-LS_1527_R1",
"buenrostro-bernstein:SS-LS_1527_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:25.126870+00:00",
"file_format": "fastq",
"file_size": 2319,
"href": "/sequence-files/IGVFFI3921HSNU/@@download/IGVFFI3921HSNU.fastq.gz",
"md5sum": "b7a0ba301df87ec19b58632f9d3de971",
"s3_uri": "s3://igvf-files/2024/02/12/047bcdda-3aae-4b8b-9695-e5363e55d330/IGVFFI3921HSNU.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-1120_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0594JHQL/",
"accession": "IGVFFI0594JHQL",
"aliases": [
"bradley-bernstein:SS-LS_1527_R2",
"buenrostro-bernstein:SS-LS_1527_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:26.093273+00:00",
"file_format": "fastq",
"file_size": 3785,
"href": "/sequence-files/IGVFFI0594JHQL/@@download/IGVFFI0594JHQL.fastq.gz",
"md5sum": "6822cacbcc96bc7c409cd9d0c4c9cc05",
"s3_uri": "s3://igvf-files/2024/02/12/68b12ac7-3f26-4578-8bab-b5715407915c/IGVFFI0594JHQL.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-1120_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1625LMBR/",
"accession": "IGVFFI1625LMBR",
"aliases": [
"bradley-bernstein:SS-LS_2389_R2",
"buenrostro-bernstein:SS-LS_2389_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:23.076758+00:00",
"file_format": "fastq",
"file_size": 433317207,
"href": "/sequence-files/IGVFFI1625LMBR/@@download/IGVFFI1625LMBR.fastq.gz",
"md5sum": "508ac033623ffdedd5061a73e214c3ab",
"s3_uri": "s3://igvf-files/2024/02/12/7176f380-6a41-4aaa-9e9a-e420396d30d5/IGVFFI1625LMBR.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-57_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4128KKPY/",
"accession": "IGVFFI4128KKPY",
"aliases": [
"bradley-bernstein:SS-LS_2293_R2",
"buenrostro-bernstein:SS-LS_2293_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:19.451965+00:00",
"file_format": "fastq",
"file_size": 431553229,
"href": "/sequence-files/IGVFFI4128KKPY/@@download/IGVFFI4128KKPY.fastq.gz",
"md5sum": "91c4c9db4365b6530b542de2d37d0614",
"s3_uri": "s3://igvf-files/2024/02/12/54a8593a-8fb6-4905-9ec2-b02440ed25e0/IGVFFI4128KKPY.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-57_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9655XHTW/",
"accession": "IGVFFI9655XHTW",
"aliases": [
"bradley-bernstein:SS-LS_1719_R1",
"buenrostro-bernstein:SS-LS_1719_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:38.238547+00:00",
"file_format": "fastq",
"file_size": 2254,
"href": "/sequence-files/IGVFFI9655XHTW/@@download/IGVFFI9655XHTW.fastq.gz",
"md5sum": "de0abc429888d85988ade2e7d528636b",
"s3_uri": "s3://igvf-files/2024/02/12/f11c6c7b-7292-4cd8-9c0d-6efcabba7705/IGVFFI9655XHTW.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-1120_L4_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
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