{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5674PNNL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5674PNNL",
"aliases": [
"bradley-bernstein:scRNA Lib 6",
"buenrostro-bernstein:scRNA Lib 6"
],
"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 [IGVFSM2165FAHM](/primary-cells/IGVFSM2165FAHM/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2165FAHM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has sequence file(s): [IGVFFI0104DBGJ](/sequence-files/IGVFFI0104DBGJ/), [IGVFFI2106FLTI](/sequence-files/IGVFFI2106FLTI/), [IGVFFI0874BAJX](/sequence-files/IGVFFI0874BAJX/), [IGVFFI3749RPPB](/sequence-files/IGVFFI3749RPPB/), [IGVFFI1748SURF](/sequence-files/IGVFFI1748SURF/), [IGVFFI3518YKVN](/sequence-files/IGVFFI3518YKVN/), [IGVFFI0046KXNZ](/sequence-files/IGVFFI0046KXNZ/), [IGVFFI2069IHGD](/sequence-files/IGVFFI2069IHGD/), [IGVFFI5896EUES](/sequence-files/IGVFFI5896EUES/), [IGVFFI4527MWCJ](/sequence-files/IGVFFI4527MWCJ/), [IGVFFI4701TPHP](/sequence-files/IGVFFI4701TPHP/), [IGVFFI0132OMEH](/sequence-files/IGVFFI0132OMEH/), [IGVFFI8354GVAX](/sequence-files/IGVFFI8354GVAX/), [IGVFFI7580NKLO](/sequence-files/IGVFFI7580NKLO/), [IGVFFI4369GCMY](/sequence-files/IGVFFI4369GCMY/), [IGVFFI9596ANCH](/sequence-files/IGVFFI9596ANCH/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI0104DBGJ](/sequence-files/IGVFFI0104DBGJ/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI2106FLTI](/sequence-files/IGVFFI2106FLTI/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI0874BAJX](/sequence-files/IGVFFI0874BAJX/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI3749RPPB](/sequence-files/IGVFFI3749RPPB/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI1748SURF](/sequence-files/IGVFFI1748SURF/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI3518YKVN](/sequence-files/IGVFFI3518YKVN/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI0046KXNZ](/sequence-files/IGVFFI0046KXNZ/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI2069IHGD](/sequence-files/IGVFFI2069IHGD/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI5896EUES](/sequence-files/IGVFFI5896EUES/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI4527MWCJ](/sequence-files/IGVFFI4527MWCJ/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI4701TPHP](/sequence-files/IGVFFI4701TPHP/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI0132OMEH](/sequence-files/IGVFFI0132OMEH/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI8354GVAX](/sequence-files/IGVFFI8354GVAX/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI7580NKLO](/sequence-files/IGVFFI7580NKLO/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI4369GCMY](/sequence-files/IGVFFI4369GCMY/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) has a sequence file [IGVFFI9596ANCH](/sequence-files/IGVFFI9596ANCH/) 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/IGVFDS5674PNNL/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS5674PNNL](/measurement-sets/IGVFDS5674PNNL/) 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/IGVFDS5674PNNL/"
}
]
},
"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": "2024-02-12T21:13:12.270126+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8099ZPMK/",
"accession": "IGVFDO8099ZPMK",
"aliases": [
"bradley-bernstein:Donor 1507",
"buenrostro-bernstein:Donor 1507"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0104DBGJ/",
"accession": "IGVFFI0104DBGJ",
"aliases": [
"bradley-bernstein:SS-LS_2536_R2",
"buenrostro-bernstein:SS-LS_2536_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:56.445545+00:00",
"file_format": "fastq",
"file_size": 2330124653,
"href": "/sequence-files/IGVFFI0104DBGJ/@@download/IGVFFI0104DBGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/448f626e-5dbf-4958-819c-455edb03f795/IGVFFI0104DBGJ.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-12_L4_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2106FLTI/",
"accession": "IGVFFI2106FLTI",
"aliases": [
"bradley-bernstein:SS-LS_1674_R2",
"buenrostro-bernstein:SS-LS_1674_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:57.087478+00:00",
"file_format": "fastq",
"file_size": 3107592149,
"href": "/sequence-files/IGVFFI2106FLTI/@@download/IGVFFI2106FLTI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ae93f41c-e858-43c3-98b1-4cb4184d3234/IGVFFI2106FLTI.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-1075_L4_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0874BAJX/",
"accession": "IGVFFI0874BAJX",
"aliases": [
"bradley-bernstein:SS-LS_1578_R2",
"buenrostro-bernstein:SS-LS_1578_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:18.679757+00:00",
"file_format": "fastq",
"file_size": 3098717968,
"href": "/sequence-files/IGVFFI0874BAJX/@@download/IGVFFI0874BAJX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6fe41e87-3059-466f-b3a9-1f9c32a709a8/IGVFFI0874BAJX.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-1075_L3_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3749RPPB/",
"accession": "IGVFFI3749RPPB",
"aliases": [
"bradley-bernstein:SS-LS_1386_R2",
"buenrostro-bernstein:SS-LS_1386_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:03.370333+00:00",
"file_format": "fastq",
"file_size": 3141471791,
"href": "/sequence-files/IGVFFI3749RPPB/@@download/IGVFFI3749RPPB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/dbd9c589-8cac-4f03-9273-b46cd914d87f/IGVFFI3749RPPB.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-1075_L1_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1748SURF/",
"accession": "IGVFFI1748SURF",
"aliases": [
"bradley-bernstein:SS-LS_1386_R1",
"buenrostro-bernstein:SS-LS_1386_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:02.265936+00:00",
"file_format": "fastq",
"file_size": 1147423951,
"href": "/sequence-files/IGVFFI1748SURF/@@download/IGVFFI1748SURF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3630cb16-ff13-4e8f-a6cc-5f1cc61c0b44/IGVFFI1748SURF.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-1075_L1_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3518YKVN/",
"accession": "IGVFFI3518YKVN",
"aliases": [
"bradley-bernstein:SS-LS_1674_R1",
"buenrostro-bernstein:SS-LS_1674_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:55.106651+00:00",
"file_format": "fastq",
"file_size": 1118502564,
"href": "/sequence-files/IGVFFI3518YKVN/@@download/IGVFFI3518YKVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/dd58b68c-83ac-4496-9332-e6c98e4ae3a6/IGVFFI3518YKVN.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-1075_L4_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0046KXNZ/",
"accession": "IGVFFI0046KXNZ",
"aliases": [
"bradley-bernstein:SS-LS_1482_R2",
"buenrostro-bernstein:SS-LS_1482_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:40.408679+00:00",
"file_format": "fastq",
"file_size": 3186321580,
"href": "/sequence-files/IGVFFI0046KXNZ/@@download/IGVFFI0046KXNZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b622c59d-9dc5-4d08-bec0-0f1fd41e3535/IGVFFI0046KXNZ.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-1075_L2_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2069IHGD/",
"accession": "IGVFFI2069IHGD",
"aliases": [
"bradley-bernstein:SS-LS_1578_R1",
"buenrostro-bernstein:SS-LS_1578_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:17.700994+00:00",
"file_format": "fastq",
"file_size": 1127056429,
"href": "/sequence-files/IGVFFI2069IHGD/@@download/IGVFFI2069IHGD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1e40d573-0639-4157-9312-6965873b0e11/IGVFFI2069IHGD.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-1075_L3_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5896EUES/",
"accession": "IGVFFI5896EUES",
"aliases": [
"bradley-bernstein:SS-LS_2344_R2",
"buenrostro-bernstein:SS-LS_2344_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:40.064457+00:00",
"file_format": "fastq",
"file_size": 2390322724,
"href": "/sequence-files/IGVFFI5896EUES/@@download/IGVFFI5896EUES.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e9d8b575-3e58-40e1-ab53-29b548c76631/IGVFFI5896EUES.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-12_L2_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4527MWCJ/",
"accession": "IGVFFI4527MWCJ",
"aliases": [
"bradley-bernstein:SS-LS_2248_R2",
"buenrostro-bernstein:SS-LS_2248_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:00.452640+00:00",
"file_format": "fastq",
"file_size": 2393197777,
"href": "/sequence-files/IGVFFI4527MWCJ/@@download/IGVFFI4527MWCJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6d6d9e6e-83c1-48e3-a7f3-72959b232e86/IGVFFI4527MWCJ.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-12_L1_SS-PKR-1_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4701TPHP/",
"accession": "IGVFFI4701TPHP",
"aliases": [
"bradley-bernstein:SS-LS_1482_R1",
"buenrostro-bernstein:SS-LS_1482_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:39.395771+00:00",
"file_format": "fastq",
"file_size": 1166182526,
"href": "/sequence-files/IGVFFI4701TPHP/@@download/IGVFFI4701TPHP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a983ecaa-879e-4ac3-9201-ae21c74df725/IGVFFI4701TPHP.fastq.gz",
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