{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7165EWYS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7165EWYS",
"aliases": [
"bradley-bernstein:scRNA Lib 34",
"buenrostro-bernstein:scRNA Lib 34"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM1036KMAA](/primary-cells/IGVFSM1036KMAA/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM1036KMAA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has sequence file(s): [IGVFFI1510SDIV](/sequence-files/IGVFFI1510SDIV/), [IGVFFI8544JEMA](/sequence-files/IGVFFI8544JEMA/), [IGVFFI6152KSZH](/sequence-files/IGVFFI6152KSZH/), [IGVFFI0140WECC](/sequence-files/IGVFFI0140WECC/), [IGVFFI6661QSWA](/sequence-files/IGVFFI6661QSWA/), [IGVFFI0116MQAG](/sequence-files/IGVFFI0116MQAG/), [IGVFFI1395ISJZ](/sequence-files/IGVFFI1395ISJZ/), [IGVFFI5751MCCX](/sequence-files/IGVFFI5751MCCX/), [IGVFFI1601HUAU](/sequence-files/IGVFFI1601HUAU/), [IGVFFI2037WBYB](/sequence-files/IGVFFI2037WBYB/), [IGVFFI2206GYBJ](/sequence-files/IGVFFI2206GYBJ/), [IGVFFI4573EWPG](/sequence-files/IGVFFI4573EWPG/), [IGVFFI9809NFJF](/sequence-files/IGVFFI9809NFJF/), [IGVFFI5003ULHK](/sequence-files/IGVFFI5003ULHK/), [IGVFFI0140EWDU](/sequence-files/IGVFFI0140EWDU/), [IGVFFI3990CWMZ](/sequence-files/IGVFFI3990CWMZ/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI1510SDIV](/sequence-files/IGVFFI1510SDIV/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI8544JEMA](/sequence-files/IGVFFI8544JEMA/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI6152KSZH](/sequence-files/IGVFFI6152KSZH/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI0140WECC](/sequence-files/IGVFFI0140WECC/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI6661QSWA](/sequence-files/IGVFFI6661QSWA/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI0116MQAG](/sequence-files/IGVFFI0116MQAG/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI1395ISJZ](/sequence-files/IGVFFI1395ISJZ/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI5751MCCX](/sequence-files/IGVFFI5751MCCX/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI1601HUAU](/sequence-files/IGVFFI1601HUAU/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI2037WBYB](/sequence-files/IGVFFI2037WBYB/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI2206GYBJ](/sequence-files/IGVFFI2206GYBJ/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI4573EWPG](/sequence-files/IGVFFI4573EWPG/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI9809NFJF](/sequence-files/IGVFFI9809NFJF/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI5003ULHK](/sequence-files/IGVFFI5003ULHK/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI0140EWDU](/sequence-files/IGVFFI0140EWDU/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) has a sequence file [IGVFFI3990CWMZ](/sequence-files/IGVFFI3990CWMZ/) 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/IGVFDS7165EWYS/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS7165EWYS](/measurement-sets/IGVFDS7165EWYS/) 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/IGVFDS7165EWYS/"
}
]
},
"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": "2024-02-12T21:12:58.198776+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8549ATSE/",
"accession": "IGVFDO8549ATSE",
"aliases": [
"bradley-bernstein:Donor 1511",
"buenrostro-bernstein:Donor 1511"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1510SDIV/",
"accession": "IGVFFI1510SDIV",
"aliases": [
"bradley-bernstein:SS-LS_1442_R1",
"buenrostro-bernstein:SS-LS_1442_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:09.146773+00:00",
"file_format": "fastq",
"file_size": 497367067,
"href": "/sequence-files/IGVFFI1510SDIV/@@download/IGVFFI1510SDIV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5d6d6803-5751-4ca5-bdfe-edec4fc6452d/IGVFFI1510SDIV.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-1131_L1_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8544JEMA/",
"accession": "IGVFFI8544JEMA",
"aliases": [
"bradley-bernstein:SS-LS_1442_R2",
"buenrostro-bernstein:SS-LS_1442_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:10.097862+00:00",
"file_format": "fastq",
"file_size": 1192967440,
"href": "/sequence-files/IGVFFI8544JEMA/@@download/IGVFFI8544JEMA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/06de2293-d4ae-4536-a00d-89c07cbf4bfe/IGVFFI8544JEMA.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-1131_L1_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6152KSZH/",
"accession": "IGVFFI6152KSZH",
"aliases": [
"bradley-bernstein:SS-LS_1634_R1",
"buenrostro-bernstein:SS-LS_1634_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:46.262998+00:00",
"file_format": "fastq",
"file_size": 494134292,
"href": "/sequence-files/IGVFFI6152KSZH/@@download/IGVFFI6152KSZH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/347d1f9b-9309-4a56-acf8-092e46590040/IGVFFI6152KSZH.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-1131_L3_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0140WECC/",
"accession": "IGVFFI0140WECC",
"aliases": [
"bradley-bernstein:SS-LS_2400_R2",
"buenrostro-bernstein:SS-LS_2400_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:35.297198+00:00",
"file_format": "fastq",
"file_size": 626457712,
"href": "/sequence-files/IGVFFI0140WECC/@@download/IGVFFI0140WECC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b2faa2d3-84bc-4de9-b7fd-991ae0e9ae0c/IGVFFI0140WECC.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-68_L2_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6661QSWA/",
"accession": "IGVFFI6661QSWA",
"aliases": [
"bradley-bernstein:SS-LS_1730_R1",
"buenrostro-bernstein:SS-LS_1730_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:22.571168+00:00",
"file_format": "fastq",
"file_size": 507539311,
"href": "/sequence-files/IGVFFI6661QSWA/@@download/IGVFFI6661QSWA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/bff90d27-97c4-4ed8-9651-ef14242f023f/IGVFFI6661QSWA.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-1131_L4_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0116MQAG/",
"accession": "IGVFFI0116MQAG",
"aliases": [
"bradley-bernstein:SS-LS_1538_R1",
"buenrostro-bernstein:SS-LS_1538_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:11.649609+00:00",
"file_format": "fastq",
"file_size": 507737119,
"href": "/sequence-files/IGVFFI0116MQAG/@@download/IGVFFI0116MQAG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/80145c32-5b5d-4b78-89c2-3914e89d6455/IGVFFI0116MQAG.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-1131_L2_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1395ISJZ/",
"accession": "IGVFFI1395ISJZ",
"aliases": [
"bradley-bernstein:SS-LS_1538_R2",
"buenrostro-bernstein:SS-LS_1538_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:12.572497+00:00",
"file_format": "fastq",
"file_size": 1221287388,
"href": "/sequence-files/IGVFFI1395ISJZ/@@download/IGVFFI1395ISJZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7aaf7da2-54d1-4aae-a18e-07a255aa7316/IGVFFI1395ISJZ.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-1131_L2_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5751MCCX/",
"accession": "IGVFFI5751MCCX",
"aliases": [
"bradley-bernstein:SS-LS_2592_R1",
"buenrostro-bernstein:SS-LS_2592_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:14.188600+00:00",
"file_format": "fastq",
"file_size": 281799208,
"href": "/sequence-files/IGVFFI5751MCCX/@@download/IGVFFI5751MCCX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e0b1c0b1-2074-4430-87d9-8be279bfbce7/IGVFFI5751MCCX.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-68_L4_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1601HUAU/",
"accession": "IGVFFI1601HUAU",
"aliases": [
"bradley-bernstein:SS-LS_1634_R2",
"buenrostro-bernstein:SS-LS_1634_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:47.213042+00:00",
"file_format": "fastq",
"file_size": 1182039540,
"href": "/sequence-files/IGVFFI1601HUAU/@@download/IGVFFI1601HUAU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6d7fedcb-d35c-406e-a216-4d6185297169/IGVFFI1601HUAU.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-1131_L3_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2037WBYB/",
"accession": "IGVFFI2037WBYB",
"aliases": [
"bradley-bernstein:SS-LS_1730_R2",
"buenrostro-bernstein:SS-LS_1730_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:23.559265+00:00",
"file_format": "fastq",
"file_size": 1220989132,
"href": "/sequence-files/IGVFFI2037WBYB/@@download/IGVFFI2037WBYB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c45f0512-11c3-47be-9339-e318e3912c5c/IGVFFI2037WBYB.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-1131_L4_SS-PKR-6_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2206GYBJ/",
"accession": "IGVFFI2206GYBJ",
"aliases": [
"bradley-bernstein:SS-LS_2496_R2",
"buenrostro-bernstein:SS-LS_2496_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:14.741157+00:00",
"file_format": "fastq",
"file_size": 619720776,
"href": "/sequence-files/IGVFFI2206GYBJ/@@download/IGVFFI2206GYBJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8fbc871f-e8df-4b71-b24a-6178d26a8f83/IGVFFI2206GYBJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
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