{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7332VBBE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7332VBBE",
"aliases": [
"bradley-bernstein:scRNA Lib 17",
"buenrostro-bernstein:scRNA Lib 17"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM9424FQXS](/primary-cells/IGVFSM9424FQXS/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM9424FQXS/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has sequence file(s): [IGVFFI7879FHCC](/sequence-files/IGVFFI7879FHCC/), [IGVFFI0964GMPX](/sequence-files/IGVFFI0964GMPX/), [IGVFFI7087DYDY](/sequence-files/IGVFFI7087DYDY/), [IGVFFI2138SPJQ](/sequence-files/IGVFFI2138SPJQ/), [IGVFFI1606HRHW](/sequence-files/IGVFFI1606HRHW/), [IGVFFI7971RAAO](/sequence-files/IGVFFI7971RAAO/), [IGVFFI7844NJPL](/sequence-files/IGVFFI7844NJPL/), [IGVFFI2965ZDQK](/sequence-files/IGVFFI2965ZDQK/), [IGVFFI5091XLLH](/sequence-files/IGVFFI5091XLLH/), [IGVFFI1357ZBRT](/sequence-files/IGVFFI1357ZBRT/), [IGVFFI0663MEAF](/sequence-files/IGVFFI0663MEAF/), [IGVFFI6597TKBW](/sequence-files/IGVFFI6597TKBW/), [IGVFFI0816BZVQ](/sequence-files/IGVFFI0816BZVQ/), [IGVFFI2691KJBJ](/sequence-files/IGVFFI2691KJBJ/), [IGVFFI5071HLSY](/sequence-files/IGVFFI5071HLSY/), [IGVFFI2877DKAS](/sequence-files/IGVFFI2877DKAS/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI7879FHCC](/sequence-files/IGVFFI7879FHCC/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI0964GMPX](/sequence-files/IGVFFI0964GMPX/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI7087DYDY](/sequence-files/IGVFFI7087DYDY/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI2138SPJQ](/sequence-files/IGVFFI2138SPJQ/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI1606HRHW](/sequence-files/IGVFFI1606HRHW/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI7971RAAO](/sequence-files/IGVFFI7971RAAO/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI7844NJPL](/sequence-files/IGVFFI7844NJPL/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI2965ZDQK](/sequence-files/IGVFFI2965ZDQK/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI5091XLLH](/sequence-files/IGVFFI5091XLLH/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI1357ZBRT](/sequence-files/IGVFFI1357ZBRT/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI0663MEAF](/sequence-files/IGVFFI0663MEAF/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI6597TKBW](/sequence-files/IGVFFI6597TKBW/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI0816BZVQ](/sequence-files/IGVFFI0816BZVQ/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI2691KJBJ](/sequence-files/IGVFFI2691KJBJ/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI5071HLSY](/sequence-files/IGVFFI5071HLSY/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has a sequence file [IGVFFI2877DKAS](/sequence-files/IGVFFI2877DKAS/) 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/IGVFDS7332VBBE/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS7332VBBE](/measurement-sets/IGVFDS7332VBBE/) has an `assay_term` of single-cell RNA sequencing assay 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/IGVFDS7332VBBE/"
}
]
},
"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": "2024-02-12T21:13:04.801556+00:00",
"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/IGVFFI7879FHCC/",
"accession": "IGVFFI7879FHCC",
"aliases": [
"bradley-bernstein:SS-LS_1408_R2",
"buenrostro-bernstein:SS-LS_1408_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:37.522165+00:00",
"file_format": "fastq",
"file_size": 1727211453,
"href": "/sequence-files/IGVFFI7879FHCC/@@download/IGVFFI7879FHCC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4892738b-3135-4716-b296-73769c3c07bc/IGVFFI7879FHCC.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-1097_L1_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0964GMPX/",
"accession": "IGVFFI0964GMPX",
"aliases": [
"bradley-bernstein:SS-LS_2462_R1",
"buenrostro-bernstein:SS-LS_2462_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:53.831762+00:00",
"file_format": "fastq",
"file_size": 298536263,
"href": "/sequence-files/IGVFFI0964GMPX/@@download/IGVFFI0964GMPX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/14b31c24-2cfc-4f02-8131-70aff91e2d7b/IGVFFI0964GMPX.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-34_L3_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7087DYDY/",
"accession": "IGVFFI7087DYDY",
"aliases": [
"bradley-bernstein:SS-LS_2270_R2",
"buenrostro-bernstein:SS-LS_2270_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:13.464120+00:00",
"file_format": "fastq",
"file_size": 618471552,
"href": "/sequence-files/IGVFFI7087DYDY/@@download/IGVFFI7087DYDY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1de06e4f-e268-476d-8647-30cfcac9fda5/IGVFFI7087DYDY.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-34_L1_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2138SPJQ/",
"accession": "IGVFFI2138SPJQ",
"aliases": [
"bradley-bernstein:SS-LS_2366_R2",
"buenrostro-bernstein:SS-LS_2366_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:49.302381+00:00",
"file_format": "fastq",
"file_size": 619634746,
"href": "/sequence-files/IGVFFI2138SPJQ/@@download/IGVFFI2138SPJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a5da3dd7-0c35-48f7-92f4-bafd2c2654ef/IGVFFI2138SPJQ.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-34_L2_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1606HRHW/",
"accession": "IGVFFI1606HRHW",
"aliases": [
"bradley-bernstein:SS-LS_1504_R1",
"buenrostro-bernstein:SS-LS_1504_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:17.269994+00:00",
"file_format": "fastq",
"file_size": 753339121,
"href": "/sequence-files/IGVFFI1606HRHW/@@download/IGVFFI1606HRHW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2b319815-d6d3-4364-817e-c21f7ec45c95/IGVFFI1606HRHW.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-1097_L2_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7971RAAO/",
"accession": "IGVFFI7971RAAO",
"aliases": [
"bradley-bernstein:SS-LS_1696_R1",
"buenrostro-bernstein:SS-LS_1696_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:31.984593+00:00",
"file_format": "fastq",
"file_size": 754193144,
"href": "/sequence-files/IGVFFI7971RAAO/@@download/IGVFFI7971RAAO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/894f1130-2271-466b-a25c-a7c9c679979a/IGVFFI7971RAAO.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-1097_L4_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7844NJPL/",
"accession": "IGVFFI7844NJPL",
"aliases": [
"bradley-bernstein:SS-LS_2366_R1",
"buenrostro-bernstein:SS-LS_2366_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:48.396855+00:00",
"file_format": "fastq",
"file_size": 299593262,
"href": "/sequence-files/IGVFFI7844NJPL/@@download/IGVFFI7844NJPL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b92e88fb-82b1-4146-a7c5-335599b7ac44/IGVFFI7844NJPL.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-34_L2_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2965ZDQK/",
"accession": "IGVFFI2965ZDQK",
"aliases": [
"bradley-bernstein:SS-LS_1408_R1",
"buenrostro-bernstein:SS-LS_1408_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:36.560723+00:00",
"file_format": "fastq",
"file_size": 743662571,
"href": "/sequence-files/IGVFFI2965ZDQK/@@download/IGVFFI2965ZDQK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/18e6e570-c652-451a-ad08-88aa26286b3c/IGVFFI2965ZDQK.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-1097_L1_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5091XLLH/",
"accession": "IGVFFI5091XLLH",
"aliases": [
"bradley-bernstein:SS-LS_1696_R2",
"buenrostro-bernstein:SS-LS_1696_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:33.126902+00:00",
"file_format": "fastq",
"file_size": 1753223483,
"href": "/sequence-files/IGVFFI5091XLLH/@@download/IGVFFI5091XLLH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3d59f880-f1de-4241-91b4-0de7801ab199/IGVFFI5091XLLH.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-1097_L4_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1357ZBRT/",
"accession": "IGVFFI1357ZBRT",
"aliases": [
"bradley-bernstein:SS-LS_1504_R2",
"buenrostro-bernstein:SS-LS_1504_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:18.367815+00:00",
"file_format": "fastq",
"file_size": 1751765817,
"href": "/sequence-files/IGVFFI1357ZBRT/@@download/IGVFFI1357ZBRT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7eb39895-10a3-4938-9c5d-fd970f48152e/IGVFFI1357ZBRT.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-1097_L2_SS-PKR-3_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0663MEAF/",
"accession": "IGVFFI0663MEAF",
"aliases": [
"bradley-bernstein:SS-LS_1600_R1",
"buenrostro-bernstein:SS-LS_1600_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:54.411521+00:00",
"file_format": "fastq",
"file_size": 741571665,
"href": "/sequence-files/IGVFFI0663MEAF/@@download/IGVFFI0663MEAF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0d36a005-5429-4bd2-bd19-eb3d106dc7da/IGVFFI0663MEAF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
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