{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4275VNMS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4275VNMS",
"aliases": [
"chongyuan-luo:ys3g_snATAC"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4275VNMS](/measurement-sets/IGVFDS4275VNMS/) 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/IGVFDS4275VNMS/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7968DCLN](/multiplexed-samples/IGVFSM7968DCLN/) 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/IGVFSM7968DCLN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4275VNMS](/measurement-sets/IGVFDS4275VNMS/) 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/IGVFDS4275VNMS/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS4275VNMS](/measurement-sets/IGVFDS4275VNMS/) 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/IGVFDS4275VNMS/"
}
]
},
"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": "2024-11-15T19:32:20.058961+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/IGVFDO2328XGNY/",
"accession": "IGVFDO2328XGNY",
"aliases": [
"chongyuan-luo:C38"
],
"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/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/IGVFFI2494WHLS/",
"accession": "IGVFFI2494WHLS",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:51:23.023175+00:00",
"file_format": "fastq",
"file_size": 2245042386,
"href": "/sequence-files/IGVFFI2494WHLS/@@download/IGVFFI2494WHLS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/79c71e46-5c1c-4a7c-966a-1eeb3d7a018c/IGVFFI2494WHLS.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/atac/IGVF2ATAC_G_S7_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2252FYMJ/",
"accession": "IGVFFI2252FYMJ",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:39:47.932271+00:00",
"file_format": "fastq",
"file_size": 2269435076,
"href": "/sequence-files/IGVFFI2252FYMJ/@@download/IGVFFI2252FYMJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/9640a8a8-30b8-4970-a82e-fd0184efb5ed/IGVFFI2252FYMJ.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/atac/IGVF2ATAC_G_S7_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7476DXMY/",
"accession": "IGVFFI7476DXMY",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L2_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:46:34.533198+00:00",
"file_format": "fastq",
"file_size": 17868971191,
"href": "/sequence-files/IGVFFI7476DXMY/@@download/IGVFFI7476DXMY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/eefb6e11-3a50-43a8-9886-6344e887d6af/IGVFFI7476DXMY.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/atac/IGVF2ATAC_G_S7_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5221QVXJ/",
"accession": "IGVFFI5221QVXJ",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:45:01.853123+00:00",
"file_format": "fastq",
"file_size": 5537918331,
"href": "/sequence-files/IGVFFI5221QVXJ/@@download/IGVFFI5221QVXJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/36f5d8ea-6c14-40b9-9e07-70752a5564e8/IGVFFI5221QVXJ.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/atac/IGVF2ATAC_G_S7_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0942KGEP/",
"accession": "IGVFFI0942KGEP",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:52:03.753666+00:00",
"file_format": "fastq",
"file_size": 16785518388,
"href": "/sequence-files/IGVFFI0942KGEP/@@download/IGVFFI0942KGEP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/9e6bff77-e38d-4856-b432-d6c9401adfad/IGVFFI0942KGEP.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/atac/IGVF2ATAC_G_S7_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1265JCFG/",
"accession": "IGVFFI1265JCFG",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:56:33.859547+00:00",
"file_format": "fastq",
"file_size": 5481750443,
"href": "/sequence-files/IGVFFI1265JCFG/@@download/IGVFFI1265JCFG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/c4322ef1-4993-4181-8798-fc136c535b92/IGVFFI1265JCFG.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/atac/IGVF2ATAC_G_S7_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7086BBQA/",
"accession": "IGVFFI7086BBQA",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L3_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:58:05.101714+00:00",
"file_format": "fastq",
"file_size": 17730779485,
"href": "/sequence-files/IGVFFI7086BBQA/@@download/IGVFFI7086BBQA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/4362035a-c775-4511-8967-53fbb92fab04/IGVFFI7086BBQA.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/atac/IGVF2ATAC_G_S7_L003_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4179OBQD/",
"accession": "IGVFFI4179OBQD",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-04T23:40:29.206237+00:00",
"file_format": "fastq",
"file_size": 16969499275,
"href": "/sequence-files/IGVFFI4179OBQD/@@download/IGVFFI4179OBQD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/04/3735c254-be03-416a-a44d-b2688642dbb1/IGVFFI4179OBQD.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/atac/IGVF2ATAC_G_S7_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8025OWTD/",
"accession": "IGVFFI8025OWTD",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L2_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-19T00:08:59.881796+00:00",
"file_format": "yaml",
"file_size": 1295,
"href": "/configuration-files/IGVFFI8025OWTD/@@download/IGVFFI8025OWTD.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/19/0041eb92-752c-49c0-bc50-27d989bdc6b7/IGVFFI8025OWTD.yaml.gz",
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/yaml/year2/multiome/atac/ys3g.L2.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7852PGPM/",
"accession": "IGVFFI7852PGPM",
"aliases": [
"chongyuan-luo:ys3g_snATAC_L3_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-19T00:09:34.062611+00:00",
"file_format": "yaml",
"file_size": 1296,
"href": "/configuration-files/IGVFFI7852PGPM/@@download/IGVFFI7852PGPM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/19/0611ddc9-1a57-4182-8e36-4a1a9e7bfd0d/IGVFFI7852PGPM.yaml.gz",
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/yaml/year2/multiome/atac/ys3g.L3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/kathrin-plath/",
"title": "Kathrin Plath, UCLA"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"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/IGVFDS9374IPYD/",
"accession": "IGVFDS9374IPYD",
"status": "released"
}
],
"release_timestamp": "2025-03-27T21:33:33.611838+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7968DCLN/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7968DCLN",
"aliases": [
"chongyuan-luo:ys3g_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 12 days; Homo sapiens fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 14 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": "2025-02-04T23:39:47.932271+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "150719fc-85dd-4150-a08f-11d44af6b87f"
}