{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8938MFTZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8938MFTZ",
"aliases": [
"bradley-bernstein:scATAC Lib 5",
"buenrostro-bernstein:scATAC Lib 5"
],
"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 [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) 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/IGVFDS8938MFTZ/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM8523CFBV](/primary-cells/IGVFSM8523CFBV/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM8523CFBV/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM8523CFBV](/primary-cells/IGVFSM8523CFBV/) 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/IGVFSM8523CFBV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has sequence file(s): [IGVFFI5464FGXS](/sequence-files/IGVFFI5464FGXS/), [IGVFFI8221VFKO](/sequence-files/IGVFFI8221VFKO/), [IGVFFI5524JBHE](/sequence-files/IGVFFI5524JBHE/), [IGVFFI3214UMBS](/sequence-files/IGVFFI3214UMBS/), [IGVFFI4870YIUH](/sequence-files/IGVFFI4870YIUH/), [IGVFFI5707ZXAA](/sequence-files/IGVFFI5707ZXAA/), [IGVFFI5015XTEQ](/sequence-files/IGVFFI5015XTEQ/), [IGVFFI4963CCPQ](/sequence-files/IGVFFI4963CCPQ/), [IGVFFI4589LANI](/sequence-files/IGVFFI4589LANI/), [IGVFFI3001FIYK](/sequence-files/IGVFFI3001FIYK/), [IGVFFI5040DTDV](/sequence-files/IGVFFI5040DTDV/), [IGVFFI8405TYBH](/sequence-files/IGVFFI8405TYBH/), [IGVFFI4467JEMT](/sequence-files/IGVFFI4467JEMT/), [IGVFFI0322TNPU](/sequence-files/IGVFFI0322TNPU/), [IGVFFI0233JOEQ](/sequence-files/IGVFFI0233JOEQ/), [IGVFFI9647ZOWN](/sequence-files/IGVFFI9647ZOWN/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI5464FGXS](/sequence-files/IGVFFI5464FGXS/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI8221VFKO](/sequence-files/IGVFFI8221VFKO/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI5524JBHE](/sequence-files/IGVFFI5524JBHE/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI3214UMBS](/sequence-files/IGVFFI3214UMBS/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI4870YIUH](/sequence-files/IGVFFI4870YIUH/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI5707ZXAA](/sequence-files/IGVFFI5707ZXAA/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI5015XTEQ](/sequence-files/IGVFFI5015XTEQ/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI4963CCPQ](/sequence-files/IGVFFI4963CCPQ/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI4589LANI](/sequence-files/IGVFFI4589LANI/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI3001FIYK](/sequence-files/IGVFFI3001FIYK/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI5040DTDV](/sequence-files/IGVFFI5040DTDV/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI8405TYBH](/sequence-files/IGVFFI8405TYBH/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI4467JEMT](/sequence-files/IGVFFI4467JEMT/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI0322TNPU](/sequence-files/IGVFFI0322TNPU/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI0233JOEQ](/sequence-files/IGVFFI0233JOEQ/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) has a sequence file [IGVFFI9647ZOWN](/sequence-files/IGVFFI9647ZOWN/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) 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/IGVFDS8938MFTZ/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8938MFTZ](/measurement-sets/IGVFDS8938MFTZ/) 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/IGVFDS8938MFTZ/"
}
]
},
"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": "2024-02-12T21:13:00.941216+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/IGVFFI5464FGXS/",
"accession": "IGVFFI5464FGXS",
"aliases": [
"bradley-bernstein:SS-LS_1575_R2",
"buenrostro-bernstein:SS-LS_1575_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:45.409569+00:00",
"file_format": "fastq",
"file_size": 143909,
"href": "/sequence-files/IGVFFI5464FGXS/@@download/IGVFFI5464FGXS.fastq.gz",
"md5sum": "5ecde084bc59f976f511d99225c1fceb",
"s3_uri": "s3://igvf-files/2024/02/12/9197f5c0-4de5-44a6-8596-29a2fab34210/IGVFFI5464FGXS.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-1072_L3_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8221VFKO/",
"accession": "IGVFFI8221VFKO",
"aliases": [
"bradley-bernstein:SS-LS_1383_R1",
"buenrostro-bernstein:SS-LS_1383_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:26.775294+00:00",
"file_format": "fastq",
"file_size": 62790,
"href": "/sequence-files/IGVFFI8221VFKO/@@download/IGVFFI8221VFKO.fastq.gz",
"md5sum": "632fcf3b25b5ef2576e6f2b5e6eeecae",
"s3_uri": "s3://igvf-files/2024/02/12/14d8d9e6-e38b-479c-bdcb-91de51ae3d25/IGVFFI8221VFKO.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-1072_L1_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5524JBHE/",
"accession": "IGVFFI5524JBHE",
"aliases": [
"bradley-bernstein:SS-LS_1383_R2",
"buenrostro-bernstein:SS-LS_1383_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:27.977205+00:00",
"file_format": "fastq",
"file_size": 136418,
"href": "/sequence-files/IGVFFI5524JBHE/@@download/IGVFFI5524JBHE.fastq.gz",
"md5sum": "ddbff8ae67d5b3b85ebafbdea50e3e84",
"s3_uri": "s3://igvf-files/2024/02/12/e530557f-671d-4bbd-8073-8bee8a9b09c1/IGVFFI5524JBHE.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-1072_L1_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3214UMBS/",
"accession": "IGVFFI3214UMBS",
"aliases": [
"bradley-bernstein:SS-LS_1575_R1",
"buenrostro-bernstein:SS-LS_1575_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:44.380751+00:00",
"file_format": "fastq",
"file_size": 65268,
"href": "/sequence-files/IGVFFI3214UMBS/@@download/IGVFFI3214UMBS.fastq.gz",
"md5sum": "13bddbcbd7f640f9b19756342827e1fb",
"s3_uri": "s3://igvf-files/2024/02/12/8e711cc4-93ea-4c25-87c0-a6bcc077c21b/IGVFFI3214UMBS.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-1072_L3_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4870YIUH/",
"accession": "IGVFFI4870YIUH",
"aliases": [
"bradley-bernstein:SS-LS_1671_R1",
"buenrostro-bernstein:SS-LS_1671_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:21.689051+00:00",
"file_format": "fastq",
"file_size": 53394,
"href": "/sequence-files/IGVFFI4870YIUH/@@download/IGVFFI4870YIUH.fastq.gz",
"md5sum": "8a30563b689a3fac5078a0fa8166a892",
"s3_uri": "s3://igvf-files/2024/02/12/4de429a3-fc2a-4103-a6d8-ec5d32c10774/IGVFFI4870YIUH.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-1072_L4_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5707ZXAA/",
"accession": "IGVFFI5707ZXAA",
"aliases": [
"bradley-bernstein:SS-LS_2437_R1",
"buenrostro-bernstein:SS-LS_2437_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:39.588508+00:00",
"file_format": "fastq",
"file_size": 588909388,
"href": "/sequence-files/IGVFFI5707ZXAA/@@download/IGVFFI5707ZXAA.fastq.gz",
"md5sum": "3f61387bf23f8a2897e02a191cc7e84b",
"s3_uri": "s3://igvf-files/2024/02/12/82a907c9-0606-485f-8dd0-d4665dbdfe94/IGVFFI5707ZXAA.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-9_L3_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5015XTEQ/",
"accession": "IGVFFI5015XTEQ",
"aliases": [
"bradley-bernstein:SS-LS_1479_R2",
"buenrostro-bernstein:SS-LS_1479_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:04.891927+00:00",
"file_format": "fastq",
"file_size": 123298,
"href": "/sequence-files/IGVFFI5015XTEQ/@@download/IGVFFI5015XTEQ.fastq.gz",
"md5sum": "c1d2dd9f2f0bc1b798feffdf82e9fa87",
"s3_uri": "s3://igvf-files/2024/02/12/5a485d36-5057-4adc-8b1e-38b2fe0678b6/IGVFFI5015XTEQ.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-1072_L2_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4963CCPQ/",
"accession": "IGVFFI4963CCPQ",
"aliases": [
"bradley-bernstein:SS-LS_1479_R1",
"buenrostro-bernstein:SS-LS_1479_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:03.632539+00:00",
"file_format": "fastq",
"file_size": 56894,
"href": "/sequence-files/IGVFFI4963CCPQ/@@download/IGVFFI4963CCPQ.fastq.gz",
"md5sum": "d8d7d8f35611cfa3f1616138499e6e3e",
"s3_uri": "s3://igvf-files/2024/02/12/75bf63f6-f3d2-4298-ae8b-811335dd8103/IGVFFI4963CCPQ.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-1072_L2_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4589LANI/",
"accession": "IGVFFI4589LANI",
"aliases": [
"bradley-bernstein:SS-LS_2341_R2",
"buenrostro-bernstein:SS-LS_2341_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:38.252826+00:00",
"file_format": "fastq",
"file_size": 1137897263,
"href": "/sequence-files/IGVFFI4589LANI/@@download/IGVFFI4589LANI.fastq.gz",
"md5sum": "94c569903abd73029384884a441eacc8",
"s3_uri": "s3://igvf-files/2024/02/12/0d7f6a72-6450-4c91-8b47-38533eca0133/IGVFFI4589LANI.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-9_L2_SS-PKR-1_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3001FIYK/",
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