{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8001MFIY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8001MFIY",
"aliases": [
"bradley-bernstein:scRNA Lib 2",
"buenrostro-bernstein:scRNA Lib 2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) 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/IGVFDS8001MFIY/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM3423JQWQ](/primary-cells/IGVFSM3423JQWQ/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM3423JQWQ/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM3423JQWQ](/primary-cells/IGVFSM3423JQWQ/) 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/IGVFSM3423JQWQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has sequence file(s): [IGVFFI6525YYFZ](/sequence-files/IGVFFI6525YYFZ/), [IGVFFI1250WWOC](/sequence-files/IGVFFI1250WWOC/), [IGVFFI2837HEEU](/sequence-files/IGVFFI2837HEEU/), [IGVFFI5949XQRA](/sequence-files/IGVFFI5949XQRA/), [IGVFFI5311IGFX](/sequence-files/IGVFFI5311IGFX/), [IGVFFI8483SZAN](/sequence-files/IGVFFI8483SZAN/), [IGVFFI4091GBZE](/sequence-files/IGVFFI4091GBZE/), [IGVFFI2519YUKX](/sequence-files/IGVFFI2519YUKX/), [IGVFFI5152YQUX](/sequence-files/IGVFFI5152YQUX/), [IGVFFI9960FWBW](/sequence-files/IGVFFI9960FWBW/), [IGVFFI4605CXSO](/sequence-files/IGVFFI4605CXSO/), [IGVFFI4777OBHH](/sequence-files/IGVFFI4777OBHH/), [IGVFFI9907NTUX](/sequence-files/IGVFFI9907NTUX/), [IGVFFI4157CKOM](/sequence-files/IGVFFI4157CKOM/), [IGVFFI0773QHKP](/sequence-files/IGVFFI0773QHKP/), [IGVFFI6406ZYGK](/sequence-files/IGVFFI6406ZYGK/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI6525YYFZ](/sequence-files/IGVFFI6525YYFZ/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI1250WWOC](/sequence-files/IGVFFI1250WWOC/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI2837HEEU](/sequence-files/IGVFFI2837HEEU/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI5949XQRA](/sequence-files/IGVFFI5949XQRA/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI5311IGFX](/sequence-files/IGVFFI5311IGFX/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI8483SZAN](/sequence-files/IGVFFI8483SZAN/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI4091GBZE](/sequence-files/IGVFFI4091GBZE/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI2519YUKX](/sequence-files/IGVFFI2519YUKX/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI5152YQUX](/sequence-files/IGVFFI5152YQUX/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI9960FWBW](/sequence-files/IGVFFI9960FWBW/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI4605CXSO](/sequence-files/IGVFFI4605CXSO/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI4777OBHH](/sequence-files/IGVFFI4777OBHH/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI9907NTUX](/sequence-files/IGVFFI9907NTUX/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI4157CKOM](/sequence-files/IGVFFI4157CKOM/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI0773QHKP](/sequence-files/IGVFFI0773QHKP/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) has a sequence file [IGVFFI6406ZYGK](/sequence-files/IGVFFI6406ZYGK/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) 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/IGVFDS8001MFIY/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8001MFIY](/measurement-sets/IGVFDS8001MFIY/) 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/IGVFDS8001MFIY/"
}
]
},
"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": "2024-02-12T21:12:29.989154+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO2605CUSL/",
"accession": "IGVFDO2605CUSL",
"aliases": [
"bradley-bernstein:Donor 1508",
"buenrostro-bernstein:Donor 1508"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6525YYFZ/",
"accession": "IGVFFI6525YYFZ",
"aliases": [
"bradley-bernstein:SS-LS_1570_R1",
"buenrostro-bernstein:SS-LS_1570_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:25.617039+00:00",
"file_format": "fastq",
"file_size": 735139057,
"href": "/sequence-files/IGVFFI6525YYFZ/@@download/IGVFFI6525YYFZ.fastq.gz",
"md5sum": "23527231304b1e5ebb2df8113ea6cb61",
"s3_uri": "s3://igvf-files/2024/02/12/3e325ede-c567-48d7-996f-a3d4cc808469/IGVFFI6525YYFZ.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-1067_L3_SS-PKR-1_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1250WWOC/",
"accession": "IGVFFI1250WWOC",
"aliases": [
"bradley-bernstein:SS-LS_1474_R1",
"buenrostro-bernstein:SS-LS_1474_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:48.475796+00:00",
"file_format": "fastq",
"file_size": 759617900,
"href": "/sequence-files/IGVFFI1250WWOC/@@download/IGVFFI1250WWOC.fastq.gz",
"md5sum": "4e07780e0362f55c8b40826c803f028c",
"s3_uri": "s3://igvf-files/2024/02/12/c98671af-8a4e-4b4c-9566-73574ce336c4/IGVFFI1250WWOC.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-1067_L2_SS-PKR-1_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2837HEEU/",
"accession": "IGVFFI2837HEEU",
"aliases": [
"bradley-bernstein:SS-LS_2528_R1",
"buenrostro-bernstein:SS-LS_2528_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:50.661792+00:00",
"file_format": "fastq",
"file_size": 610933800,
"href": "/sequence-files/IGVFFI2837HEEU/@@download/IGVFFI2837HEEU.fastq.gz",
"md5sum": "90adc36e2199b7b0ee66265db25d7fcc",
"s3_uri": "s3://igvf-files/2024/02/12/01eb1e7b-3d8a-45b2-9ac9-d2917490668e/IGVFFI2837HEEU.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-4_L4_SS-PKR-1_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5949XQRA/",
"accession": "IGVFFI5949XQRA",
"aliases": [
"bradley-bernstein:SS-LS_1378_R1",
"buenrostro-bernstein:SS-LS_1378_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:09.448334+00:00",
"file_format": "fastq",
"file_size": 748394395,
"href": "/sequence-files/IGVFFI5949XQRA/@@download/IGVFFI5949XQRA.fastq.gz",
"md5sum": "25990cda4d378c1526d9f01247e3363d",
"s3_uri": "s3://igvf-files/2024/02/12/7274c863-e101-480b-bca1-6eb6873c93fa/IGVFFI5949XQRA.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-1067_L1_SS-PKR-1_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5311IGFX/",
"accession": "IGVFFI5311IGFX",
"aliases": [
"bradley-bernstein:SS-LS_1378_R2",
"buenrostro-bernstein:SS-LS_1378_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:11.478645+00:00",
"file_format": "fastq",
"file_size": 2038938702,
"href": "/sequence-files/IGVFFI5311IGFX/@@download/IGVFFI5311IGFX.fastq.gz",
"md5sum": "b2297f0c320a9547377cdce47083f138",
"s3_uri": "s3://igvf-files/2024/02/12/f5f139f5-441e-4f22-85c5-9a2b5b9d164e/IGVFFI5311IGFX.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-1067_L1_SS-PKR-1_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8483SZAN/",
"accession": "IGVFFI8483SZAN",
"aliases": [
"bradley-bernstein:SS-LS_1474_R2",
"buenrostro-bernstein:SS-LS_1474_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:49.480325+00:00",
"file_format": "fastq",
"file_size": 2065892514,
"href": "/sequence-files/IGVFFI8483SZAN/@@download/IGVFFI8483SZAN.fastq.gz",
"md5sum": "80e4aa113fdc1a40662a06de3d58c9ab",
"s3_uri": "s3://igvf-files/2024/02/12/c65fc546-2b10-464c-848e-b0501768446f/IGVFFI8483SZAN.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-1067_L2_SS-PKR-1_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4091GBZE/",
"accession": "IGVFFI4091GBZE",
"aliases": [
"bradley-bernstein:SS-LS_1570_R2",
"buenrostro-bernstein:SS-LS_1570_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:26.547490+00:00",
"file_format": "fastq",
"file_size": 2010759439,
"href": "/sequence-files/IGVFFI4091GBZE/@@download/IGVFFI4091GBZE.fastq.gz",
"md5sum": "f1b278bc4718eea56d30ac8c9cc6a319",
"s3_uri": "s3://igvf-files/2024/02/12/50a45e83-d54a-4da7-af54-001f26864ff2/IGVFFI4091GBZE.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-1067_L3_SS-PKR-1_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2519YUKX/",
"accession": "IGVFFI2519YUKX",
"aliases": [
"bradley-bernstein:SS-LS_2432_R1",
"buenrostro-bernstein:SS-LS_2432_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:13.690668+00:00",
"file_format": "fastq",
"file_size": 624101827,
"href": "/sequence-files/IGVFFI2519YUKX/@@download/IGVFFI2519YUKX.fastq.gz",
"md5sum": "df64539981adca606efb3bbfc5550518",
"s3_uri": "s3://igvf-files/2024/02/12/4aaf42a2-a5e0-46cf-8036-266933295985/IGVFFI2519YUKX.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-4_L3_SS-PKR-1_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5152YQUX/",
"accession": "IGVFFI5152YQUX",
"aliases": [
"bradley-bernstein:SS-LS_1666_R2",
"buenrostro-bernstein:SS-LS_1666_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:01.254497+00:00",
"file_format": "fastq",
"file_size": 2011183773,
"href": "/sequence-files/IGVFFI5152YQUX/@@download/IGVFFI5152YQUX.fastq.gz",
"md5sum": "cc7b7dc723d984930d987abcf7aefc5c",
"s3_uri": "s3://igvf-files/2024/02/12/0a94f78c-1921-4240-a85a-fcafabc6890e/IGVFFI5152YQUX.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-1067_L4_SS-PKR-1_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9960FWBW/",
"accession": "IGVFFI9960FWBW",
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