{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8346OZIZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8346OZIZ",
"aliases": [
"bradley-bernstein:scATAC Lib 43",
"buenrostro-bernstein:scATAC Lib 43"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM1054BSTI](/primary-cells/IGVFSM1054BSTI/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM1054BSTI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has sequence file(s): [IGVFFI2743YRGR](/sequence-files/IGVFFI2743YRGR/), [IGVFFI2603RHCO](/sequence-files/IGVFFI2603RHCO/), [IGVFFI6232NNCJ](/sequence-files/IGVFFI6232NNCJ/), [IGVFFI4316ILMU](/sequence-files/IGVFFI4316ILMU/), [IGVFFI7685NCHI](/sequence-files/IGVFFI7685NCHI/), [IGVFFI6210AYEL](/sequence-files/IGVFFI6210AYEL/), [IGVFFI3456PKHE](/sequence-files/IGVFFI3456PKHE/), [IGVFFI5933PDFI](/sequence-files/IGVFFI5933PDFI/), [IGVFFI5783VMMI](/sequence-files/IGVFFI5783VMMI/), [IGVFFI5093QQUJ](/sequence-files/IGVFFI5093QQUJ/), [IGVFFI5891YJQB](/sequence-files/IGVFFI5891YJQB/), [IGVFFI0830MQTR](/sequence-files/IGVFFI0830MQTR/), [IGVFFI4046OIFF](/sequence-files/IGVFFI4046OIFF/), [IGVFFI1254JGCT](/sequence-files/IGVFFI1254JGCT/), [IGVFFI5938OFTG](/sequence-files/IGVFFI5938OFTG/), [IGVFFI9830RNFH](/sequence-files/IGVFFI9830RNFH/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI2743YRGR](/sequence-files/IGVFFI2743YRGR/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI2603RHCO](/sequence-files/IGVFFI2603RHCO/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI6232NNCJ](/sequence-files/IGVFFI6232NNCJ/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI4316ILMU](/sequence-files/IGVFFI4316ILMU/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI7685NCHI](/sequence-files/IGVFFI7685NCHI/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI6210AYEL](/sequence-files/IGVFFI6210AYEL/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI3456PKHE](/sequence-files/IGVFFI3456PKHE/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI5933PDFI](/sequence-files/IGVFFI5933PDFI/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI5783VMMI](/sequence-files/IGVFFI5783VMMI/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI5093QQUJ](/sequence-files/IGVFFI5093QQUJ/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI5891YJQB](/sequence-files/IGVFFI5891YJQB/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI0830MQTR](/sequence-files/IGVFFI0830MQTR/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI4046OIFF](/sequence-files/IGVFFI4046OIFF/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI1254JGCT](/sequence-files/IGVFFI1254JGCT/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI5938OFTG](/sequence-files/IGVFFI5938OFTG/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) has a sequence file [IGVFFI9830RNFH](/sequence-files/IGVFFI9830RNFH/) 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/IGVFDS8346OZIZ/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8346OZIZ](/measurement-sets/IGVFDS8346OZIZ/) 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/IGVFDS8346OZIZ/"
}
]
},
"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": [],
"creation_timestamp": "2024-02-12T21:12:28.378392+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9431XGDA/",
"accession": "IGVFDO9431XGDA",
"aliases": [
"bradley-bernstein:Donor 1506",
"buenrostro-bernstein:Donor 1506"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2743YRGR/",
"accession": "IGVFFI2743YRGR",
"aliases": [
"bradley-bernstein:SS-LS_1459_R2",
"buenrostro-bernstein:SS-LS_1459_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:51.017383+00:00",
"file_format": "fastq",
"file_size": 6101,
"href": "/sequence-files/IGVFFI2743YRGR/@@download/IGVFFI2743YRGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d09187ce-34cd-41ae-a66b-4dac051e4771/IGVFFI2743YRGR.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-1148_L1_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2603RHCO/",
"accession": "IGVFFI2603RHCO",
"aliases": [
"bradley-bernstein:SS-LS_1459_R1",
"buenrostro-bernstein:SS-LS_1459_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:50.110140+00:00",
"file_format": "fastq",
"file_size": 3258,
"href": "/sequence-files/IGVFFI2603RHCO/@@download/IGVFFI2603RHCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e407dcb2-8d0b-4282-ae40-6e6b96f1dd9e/IGVFFI2603RHCO.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-1148_L1_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6232NNCJ/",
"accession": "IGVFFI6232NNCJ",
"aliases": [
"bradley-bernstein:SS-LS_2513_R2",
"buenrostro-bernstein:SS-LS_2513_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:27.829493+00:00",
"file_format": "fastq",
"file_size": 986133430,
"href": "/sequence-files/IGVFFI6232NNCJ/@@download/IGVFFI6232NNCJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ad46db4d-34d5-40eb-99ac-20a8a6127234/IGVFFI6232NNCJ.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-85_L3_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4316ILMU/",
"accession": "IGVFFI4316ILMU",
"aliases": [
"bradley-bernstein:SS-LS_2609_R2",
"buenrostro-bernstein:SS-LS_2609_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:03.507970+00:00",
"file_format": "fastq",
"file_size": 979025510,
"href": "/sequence-files/IGVFFI4316ILMU/@@download/IGVFFI4316ILMU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f02c5601-bb63-4d6a-ac16-bfc0693bdf86/IGVFFI4316ILMU.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-85_L4_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7685NCHI/",
"accession": "IGVFFI7685NCHI",
"aliases": [
"bradley-bernstein:SS-LS_2513_R1",
"buenrostro-bernstein:SS-LS_2513_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:26.924621+00:00",
"file_format": "fastq",
"file_size": 578968020,
"href": "/sequence-files/IGVFFI7685NCHI/@@download/IGVFFI7685NCHI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f9799b0e-6fda-4126-a16e-acea50fa2532/IGVFFI7685NCHI.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-85_L3_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6210AYEL/",
"accession": "IGVFFI6210AYEL",
"aliases": [
"bradley-bernstein:SS-LS_2609_R1",
"buenrostro-bernstein:SS-LS_2609_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:02.593053+00:00",
"file_format": "fastq",
"file_size": 573271271,
"href": "/sequence-files/IGVFFI6210AYEL/@@download/IGVFFI6210AYEL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/86f3f09e-a6c0-4e10-8023-22f5307a80d8/IGVFFI6210AYEL.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-85_L4_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3456PKHE/",
"accession": "IGVFFI3456PKHE",
"aliases": [
"bradley-bernstein:SS-LS_1555_R1",
"buenrostro-bernstein:SS-LS_1555_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:07.334594+00:00",
"file_format": "fastq",
"file_size": 3306,
"href": "/sequence-files/IGVFFI3456PKHE/@@download/IGVFFI3456PKHE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a8191b0b-aa2d-440a-ba26-26242a25fb5e/IGVFFI3456PKHE.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-1148_L2_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5933PDFI/",
"accession": "IGVFFI5933PDFI",
"aliases": [
"bradley-bernstein:SS-LS_1555_R2",
"buenrostro-bernstein:SS-LS_1555_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:08.271611+00:00",
"file_format": "fastq",
"file_size": 5809,
"href": "/sequence-files/IGVFFI5933PDFI/@@download/IGVFFI5933PDFI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e34c93fc-047a-4ddb-b060-4cdfceafd179/IGVFFI5933PDFI.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-1148_L2_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5783VMMI/",
"accession": "IGVFFI5783VMMI",
"aliases": [
"bradley-bernstein:SS-LS_1651_R1",
"buenrostro-bernstein:SS-LS_1651_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:36.590196+00:00",
"file_format": "fastq",
"file_size": 2845,
"href": "/sequence-files/IGVFFI5783VMMI/@@download/IGVFFI5783VMMI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/356eba94-464b-4b37-9844-fe9f2111c464/IGVFFI5783VMMI.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-1148_L3_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5093QQUJ/",
"accession": "IGVFFI5093QQUJ",
"aliases": [
"bradley-bernstein:SS-LS_1651_R2",
"buenrostro-bernstein:SS-LS_1651_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:37.692258+00:00",
"file_format": "fastq",
"file_size": 5244,
"href": "/sequence-files/IGVFFI5093QQUJ/@@download/IGVFFI5093QQUJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/91cf2c61-1d50-4b29-bc92-451bdbb61e9b/IGVFFI5093QQUJ.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-1148_L3_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5891YJQB/",
"accession": "IGVFFI5891YJQB",
"aliases": [
"bradley-bernstein:SS-LS_1747_R1",
"buenrostro-bernstein:SS-LS_1747_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:02.229574+00:00",
"file_format": "fastq",
"file_size": 2874,
"href": "/sequence-files/IGVFFI5891YJQB/@@download/IGVFFI5891YJQB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/72365b26-177f-482d-b819-d6d1147e2357/IGVFFI5891YJQB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
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