{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4496CBBT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4496CBBT",
"aliases": [
"bradley-bernstein:scATAC Lib 21",
"buenrostro-bernstein:scATAC Lib 21"
],
"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 [IGVFSM4241TGLB](/primary-cells/IGVFSM4241TGLB/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM4241TGLB/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM4241TGLB](/primary-cells/IGVFSM4241TGLB/) 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/IGVFSM4241TGLB/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) 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/IGVFDS4496CBBT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has sequence file(s): [IGVFFI7369SOCL](/sequence-files/IGVFFI7369SOCL/), [IGVFFI1250CZMG](/sequence-files/IGVFFI1250CZMG/), [IGVFFI1138OIYQ](/sequence-files/IGVFFI1138OIYQ/), [IGVFFI7929YMCD](/sequence-files/IGVFFI7929YMCD/), [IGVFFI6131MIET](/sequence-files/IGVFFI6131MIET/), [IGVFFI5863GDKH](/sequence-files/IGVFFI5863GDKH/), [IGVFFI9018DAHW](/sequence-files/IGVFFI9018DAHW/), [IGVFFI1676AYQH](/sequence-files/IGVFFI1676AYQH/), [IGVFFI8283NBTJ](/sequence-files/IGVFFI8283NBTJ/), [IGVFFI4881CTHM](/sequence-files/IGVFFI4881CTHM/), [IGVFFI8446GRHH](/sequence-files/IGVFFI8446GRHH/), [IGVFFI0449IKMC](/sequence-files/IGVFFI0449IKMC/), [IGVFFI7597ORVA](/sequence-files/IGVFFI7597ORVA/), [IGVFFI8109INWF](/sequence-files/IGVFFI8109INWF/), [IGVFFI3108YDWE](/sequence-files/IGVFFI3108YDWE/), [IGVFFI0831DSRM](/sequence-files/IGVFFI0831DSRM/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI7369SOCL](/sequence-files/IGVFFI7369SOCL/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI1250CZMG](/sequence-files/IGVFFI1250CZMG/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI1138OIYQ](/sequence-files/IGVFFI1138OIYQ/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI7929YMCD](/sequence-files/IGVFFI7929YMCD/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI6131MIET](/sequence-files/IGVFFI6131MIET/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI5863GDKH](/sequence-files/IGVFFI5863GDKH/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI9018DAHW](/sequence-files/IGVFFI9018DAHW/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI1676AYQH](/sequence-files/IGVFFI1676AYQH/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI8283NBTJ](/sequence-files/IGVFFI8283NBTJ/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI4881CTHM](/sequence-files/IGVFFI4881CTHM/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI8446GRHH](/sequence-files/IGVFFI8446GRHH/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI0449IKMC](/sequence-files/IGVFFI0449IKMC/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI7597ORVA](/sequence-files/IGVFFI7597ORVA/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI8109INWF](/sequence-files/IGVFFI8109INWF/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI3108YDWE](/sequence-files/IGVFFI3108YDWE/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) has a sequence file [IGVFFI0831DSRM](/sequence-files/IGVFFI0831DSRM/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) 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/IGVFDS4496CBBT/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS4496CBBT](/measurement-sets/IGVFDS4496CBBT/) 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/IGVFDS4496CBBT/"
}
]
},
"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": "2024-02-12T21:12:44.194999+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO2457AMDL/",
"accession": "IGVFDO2457AMDL",
"aliases": [
"bradley-bernstein:Donor 1509",
"buenrostro-bernstein:Donor 1509"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7369SOCL/",
"accession": "IGVFFI7369SOCL",
"aliases": [
"bradley-bernstein:SS-LS_1511_R1",
"buenrostro-bernstein:SS-LS_1511_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:14.372837+00:00",
"file_format": "fastq",
"file_size": 754,
"href": "/sequence-files/IGVFFI7369SOCL/@@download/IGVFFI7369SOCL.fastq.gz",
"md5sum": "ba827845b57b5b4f8e4df9e6427c6692",
"s3_uri": "s3://igvf-files/2024/02/12/c7a686ef-95f8-463b-8a84-0a03d38880c1/IGVFFI7369SOCL.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-1104_L2_SS-PKR-4_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1250CZMG/",
"accession": "IGVFFI1250CZMG",
"aliases": [
"bradley-bernstein:SS-LS_1415_R1",
"buenrostro-bernstein:SS-LS_1415_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:38.154849+00:00",
"file_format": "fastq",
"file_size": 1355,
"href": "/sequence-files/IGVFFI1250CZMG/@@download/IGVFFI1250CZMG.fastq.gz",
"md5sum": "f75226e3da11524df5ecb62b2aaa3e2d",
"s3_uri": "s3://igvf-files/2024/02/12/e14c1d14-b724-4f67-9344-e1a0362c294d/IGVFFI1250CZMG.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-1104_L1_SS-PKR-4_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1138OIYQ/",
"accession": "IGVFFI1138OIYQ",
"aliases": [
"bradley-bernstein:SS-LS_2373_R2",
"buenrostro-bernstein:SS-LS_2373_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:10.800515+00:00",
"file_format": "fastq",
"file_size": 603102970,
"href": "/sequence-files/IGVFFI1138OIYQ/@@download/IGVFFI1138OIYQ.fastq.gz",
"md5sum": "d1a738025d0d161875861e8c5d0e56de",
"s3_uri": "s3://igvf-files/2024/02/12/08fddbea-4ce8-4b8d-96bb-5384509795cb/IGVFFI1138OIYQ.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-41_L2_SS-PKR-4_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7929YMCD/",
"accession": "IGVFFI7929YMCD",
"aliases": [
"bradley-bernstein:SS-LS_2565_R2",
"buenrostro-bernstein:SS-LS_2565_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:23.588038+00:00",
"file_format": "fastq",
"file_size": 596309252,
"href": "/sequence-files/IGVFFI7929YMCD/@@download/IGVFFI7929YMCD.fastq.gz",
"md5sum": "67dea83885eb6c71a182d8056d614236",
"s3_uri": "s3://igvf-files/2024/02/12/6b115bb3-2f5d-452a-9f6a-78bc4947274a/IGVFFI7929YMCD.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-41_L4_SS-PKR-4_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6131MIET/",
"accession": "IGVFFI6131MIET",
"aliases": [
"bradley-bernstein:SS-LS_1607_R1",
"buenrostro-bernstein:SS-LS_1607_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:52.216082+00:00",
"file_format": "fastq",
"file_size": 900,
"href": "/sequence-files/IGVFFI6131MIET/@@download/IGVFFI6131MIET.fastq.gz",
"md5sum": "0201ff5dccb6f27dbec876814420b442",
"s3_uri": "s3://igvf-files/2024/02/12/b2bff77c-dbec-44b8-ab79-35d340aaf70e/IGVFFI6131MIET.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-1104_L3_SS-PKR-4_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5863GDKH/",
"accession": "IGVFFI5863GDKH",
"aliases": [
"bradley-bernstein:SS-LS_1415_R2",
"buenrostro-bernstein:SS-LS_1415_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:39.119625+00:00",
"file_format": "fastq",
"file_size": 2384,
"href": "/sequence-files/IGVFFI5863GDKH/@@download/IGVFFI5863GDKH.fastq.gz",
"md5sum": "fa3599e18931c3e11c73eca8b11346b8",
"s3_uri": "s3://igvf-files/2024/02/12/9f6d669d-8178-44fe-875d-65398931056e/IGVFFI5863GDKH.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-1104_L1_SS-PKR-4_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9018DAHW/",
"accession": "IGVFFI9018DAHW",
"aliases": [
"bradley-bernstein:SS-LS_1511_R2",
"buenrostro-bernstein:SS-LS_1511_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:15.727802+00:00",
"file_format": "fastq",
"file_size": 1318,
"href": "/sequence-files/IGVFFI9018DAHW/@@download/IGVFFI9018DAHW.fastq.gz",
"md5sum": "4a9abd1da3a983d9cf83503dfc21a7b6",
"s3_uri": "s3://igvf-files/2024/02/12/c9a4860e-3436-45d5-a7dc-1da99d9a8411/IGVFFI9018DAHW.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-1104_L2_SS-PKR-4_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1676AYQH/",
"accession": "IGVFFI1676AYQH",
"aliases": [
"bradley-bernstein:SS-LS_1703_R1",
"buenrostro-bernstein:SS-LS_1703_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:53.241360+00:00",
"file_format": "fastq",
"file_size": 828,
"href": "/sequence-files/IGVFFI1676AYQH/@@download/IGVFFI1676AYQH.fastq.gz",
"md5sum": "d8528a463e668e70df0087ae8d60cc25",
"s3_uri": "s3://igvf-files/2024/02/12/1fa3707d-1d4f-4812-b769-c224676cb0a5/IGVFFI1676AYQH.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-1104_L4_SS-PKR-4_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8283NBTJ/",
"accession": "IGVFFI8283NBTJ",
"aliases": [
"bradley-bernstein:SS-LS_1703_R2",
"buenrostro-bernstein:SS-LS_1703_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:54.544782+00:00",
"file_format": "fastq",
"file_size": 1461,
"href": "/sequence-files/IGVFFI8283NBTJ/@@download/IGVFFI8283NBTJ.fastq.gz",
"md5sum": "799a69da2436d953f3a2ae46b5618d27",
"s3_uri": "s3://igvf-files/2024/02/12/617750e4-1bf3-4ca3-9c7a-131f0729502d/IGVFFI8283NBTJ.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-1104_L4_SS-PKR-4_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4881CTHM/",
"accession": "IGVFFI4881CTHM",
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