{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6095UGQM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6095UGQM",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003662/",
"status": "released",
"term_name": "single-nucleus methylcytosine and transcriptome sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6095UGQM](/measurement-sets/IGVFDS6095UGQM/) has sequence file(s): [IGVFFI0903RLOJ](/sequence-files/IGVFFI0903RLOJ/), [IGVFFI9627FUZW](/sequence-files/IGVFFI9627FUZW/), [IGVFFI1764HLTG](/sequence-files/IGVFFI1764HLTG/), [IGVFFI2375EELR](/sequence-files/IGVFFI2375EELR/), [IGVFFI8554WRRN](/sequence-files/IGVFFI8554WRRN/), [IGVFFI7812DGRY](/sequence-files/IGVFFI7812DGRY/), [IGVFFI2261NDGU](/sequence-files/IGVFFI2261NDGU/), [IGVFFI7971AAOY](/sequence-files/IGVFFI7971AAOY/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6095UGQM/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS6095UGQM](/measurement-sets/IGVFDS6095UGQM/) 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/IGVFDS6095UGQM/"
}
]
},
"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": [],
"creation_timestamp": "2024-11-15T19:28:32.895124+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3754NCBP/",
"accession": "IGVFDO3754NCBP",
"aliases": [
"chongyuan-luo:C29"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0903RLOJ/",
"accession": "IGVFFI0903RLOJ",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:19:18.601456+00:00",
"file_format": "fastq",
"file_size": 7176153726,
"href": "/sequence-files/IGVFFI0903RLOJ/@@download/IGVFFI0903RLOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/96db3fc9-86d4-49cd-ad28-eb6b1d1537dc/IGVFFI0903RLOJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9627FUZW/",
"accession": "IGVFFI9627FUZW",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:24:12.857737+00:00",
"file_format": "fastq",
"file_size": 7330165677,
"href": "/sequence-files/IGVFFI9627FUZW/@@download/IGVFFI9627FUZW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/16dd6c59-994f-4c59-aa85-6c05a2f6c470/IGVFFI9627FUZW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1764HLTG/",
"accession": "IGVFFI1764HLTG",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:15:17.633708+00:00",
"file_format": "fastq",
"file_size": 7444210873,
"href": "/sequence-files/IGVFFI1764HLTG/@@download/IGVFFI1764HLTG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/30799acb-7cc2-44ca-88db-356a1cabf2f0/IGVFFI1764HLTG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2375EELR/",
"accession": "IGVFFI2375EELR",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:29:12.872286+00:00",
"file_format": "fastq",
"file_size": 7496200252,
"href": "/sequence-files/IGVFFI2375EELR/@@download/IGVFFI2375EELR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/f53d7ea7-bc4f-4ab0-9759-02220e2f1288/IGVFFI2375EELR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8554WRRN/",
"accession": "IGVFFI8554WRRN",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:10:45.981410+00:00",
"file_format": "fastq",
"file_size": 7335374962,
"href": "/sequence-files/IGVFFI8554WRRN/@@download/IGVFFI8554WRRN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/19b57538-91a3-4496-9d14-55b55bfb8716/IGVFFI8554WRRN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7812DGRY/",
"accession": "IGVFFI7812DGRY",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:33:59.865151+00:00",
"file_format": "fastq",
"file_size": 7576573701,
"href": "/sequence-files/IGVFFI7812DGRY/@@download/IGVFFI7812DGRY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/c34d4dfa-0ee3-4b83-a822-bcc4c80c80e0/IGVFFI7812DGRY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2261NDGU/",
"accession": "IGVFFI2261NDGU",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:43:43.458530+00:00",
"file_format": "fastq",
"file_size": 7527277880,
"href": "/sequence-files/IGVFFI2261NDGU/@@download/IGVFFI2261NDGU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/b408a92f-721d-4e66-a066-504b90be50b8/IGVFFI2261NDGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7971AAOY/",
"accession": "IGVFFI7971AAOY",
"aliases": [
"chongyuan-luo:pgp_snmct_C29_day7_L4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T22:38:45.820873+00:00",
"file_format": "fastq",
"file_size": 7483580333,
"href": "/sequence-files/IGVFFI7971AAOY/@@download/IGVFFI7971AAOY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/4ef48494-c89b-4757-bddd-00722ce2421b/IGVFFI7971AAOY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/home/ec2-user/igvf/submit/fastq/year2/snmct/yzcl51/20231204-C29D7-Pos1-C05_S29_L004_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/chongyuan-luo/",
"title": "Chongyuan Luo, UCLA"
},
"preferred_assay_title": "snMCT-seq",
"protocols": [
"https://www.protocols.io/view/snmcat-v2-x54v9jby1g3e/v2"
],
"release_timestamp": "2025-02-11T00:54:31.583749+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4178KJPJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4178KJPJ",
"aliases": [
"chongyuan-luo:C29_day7"
],
"classifications": [
"reprogrammed cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000057/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "fibroblast",
"term_name": "fibroblast"
}
],
"status": "released",
"summary": "fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 7 days, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/EFO_0004905/",
"status": "released",
"term_name": "induced pluripotent stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "24",
"status": "released",
"submitted_by": {
"@id": "/users/ec46dfbd-fc11-419d-81e8-8ba82ffe6375/",
"title": "Terence Li"
},
"submitted_files_timestamp": "2024-11-15T22:10:45.981410+00:00",
"summary": "snMCT-seq",
"uuid": "adf08083-37b7-4469-aa34-11d4dd207a7e"
}