{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0328BSUV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0328BSUV",
"aliases": [
"chongyuan-luo:ys3j_snRNA"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0328BSUV](/measurement-sets/IGVFDS0328BSUV/) 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/IGVFDS0328BSUV/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM6738ETRL](/multiplexed-samples/IGVFSM6738ETRL/) 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": "/multiplexed-samples/IGVFSM6738ETRL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0328BSUV](/measurement-sets/IGVFDS0328BSUV/) 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/IGVFDS0328BSUV/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS0328BSUV](/measurement-sets/IGVFDS0328BSUV/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS0328BSUV/"
}
]
},
"award": {
"@id": "/awards/HG012079/",
"component": "networks",
"contact_pi": {
"@id": "/users/53ea51d1-5c61-4f1e-99fb-ef857bd652a3/",
"title": "Chongyuan Luo"
},
"title": "Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotency"
},
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2024-11-15T19:32:22.122307+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO3754NCBP/",
"accession": "IGVFDO3754NCBP",
"aliases": [
"chongyuan-luo:C29"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0351NYZH/",
"accession": "IGVFDO0351NYZH",
"aliases": [
"chongyuan-luo:C37"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2328XGNY/",
"accession": "IGVFDO2328XGNY",
"aliases": [
"chongyuan-luo:C38"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4068JJIT/",
"accession": "IGVFDO4068JJIT",
"aliases": [
"chongyuan-luo:C39"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2732QRRN/",
"accession": "IGVFFI2732QRRN",
"aliases": [
"chongyuan-luo:ys3j_snRNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-05T19:19:52.943432+00:00",
"file_format": "fastq",
"file_size": 23030928235,
"href": "/sequence-files/IGVFFI2732QRRN/@@download/IGVFFI2732QRRN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/05/ddaf655e-f897-4800-b9e2-4662896cadf7/IGVFFI2732QRRN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/multiome/gex/IGVF2GEX-J_S10_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1896SUWY/",
"accession": "IGVFFI1896SUWY",
"aliases": [
"chongyuan-luo:ys3j_snRNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-05T19:26:00.647835+00:00",
"file_format": "fastq",
"file_size": 18366264036,
"href": "/sequence-files/IGVFFI1896SUWY/@@download/IGVFFI1896SUWY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/05/0b96af9a-c59e-4933-982b-a3d1cfc3c071/IGVFFI1896SUWY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/multiome/gex/IGVF2GEX-J_S10_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0824PAXM/",
"accession": "IGVFFI0824PAXM",
"aliases": [
"chongyuan-luo:ys3j_snRNA_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-09T22:10:03.387242+00:00",
"file_format": "yaml",
"file_size": 1403,
"href": "/configuration-files/IGVFFI0824PAXM/@@download/IGVFFI0824PAXM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/09/ca7035d0-001b-4946-b7c9-914bbf5d41b0/IGVFFI0824PAXM.yaml.gz",
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/yaml/year2/multiome//rna/ys3j.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/kathrin-plath/",
"title": "Kathrin Plath, UCLA"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI8751YQRY/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome",
"protocols": [
"https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS8199DMOG/",
"accession": "IGVFDS8199DMOG",
"status": "released"
}
],
"release_timestamp": "2025-03-27T21:33:25.730352+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM6738ETRL/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6738ETRL",
"aliases": [
"chongyuan-luo:ys3j_mux"
],
"classifications": [
"reprogrammed cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/18b2e0b6-edec-475b-af8a-0afc04fa43d7/",
"certificate_identifier": "IP107-02",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000057/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "fibroblast",
"term_name": "fibroblast"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 16 days; Homo sapiens fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 18 days; ... and 2 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/ec46dfbd-fc11-419d-81e8-8ba82ffe6375/",
"title": "Terence Li"
},
"submitted_files_timestamp": "2025-02-05T19:19:52.943432+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "318c77ce-5a6d-42ef-9dd7-a0e5e41b6c9d"
}