{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9238PCPJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9238PCPJ",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003662/",
"assay_slims": [
"multiome"
],
"status": "released",
"term_name": "single-nucleus methylcytosine and transcriptome sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1171PVMI](/in-vitro-systems/IGVFSM1171PVMI/) 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": "/in-vitro-systems/IGVFSM1171PVMI/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9238PCPJ](/measurement-sets/IGVFDS9238PCPJ/) 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/IGVFDS9238PCPJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9238PCPJ](/measurement-sets/IGVFDS9238PCPJ/) has sequence file(s): [IGVFFI2283PZAK](/sequence-files/IGVFFI2283PZAK/), [IGVFFI7929HVUQ](/sequence-files/IGVFFI7929HVUQ/), [IGVFFI6160UXFK](/sequence-files/IGVFFI6160UXFK/), [IGVFFI5043EYRM](/sequence-files/IGVFFI5043EYRM/), [IGVFFI9860QJDJ](/sequence-files/IGVFFI9860QJDJ/), [IGVFFI1096BKKU](/sequence-files/IGVFFI1096BKKU/), [IGVFFI9682HXQV](/sequence-files/IGVFFI9682HXQV/), [IGVFFI0754NCXT](/sequence-files/IGVFFI0754NCXT/) 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/IGVFDS9238PCPJ/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS9238PCPJ](/measurement-sets/IGVFDS9238PCPJ/) 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/IGVFDS9238PCPJ/"
}
]
},
"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": "2024-11-15T19:28:36.256229+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO2328XGNY/",
"accession": "IGVFDO2328XGNY",
"aliases": [
"chongyuan-luo:C38"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2283PZAK/",
"accession": "IGVFFI2283PZAK",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T15:26:58.507254+00:00",
"file_format": "fastq",
"file_size": 5214923437,
"href": "/sequence-files/IGVFFI2283PZAK/@@download/IGVFFI2283PZAK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/292b0c5a-c1d0-4f57-ac55-52d11ab2ff72/IGVFFI2283PZAK.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-C38D5-Pos1-A11_S11_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7929HVUQ/",
"accession": "IGVFFI7929HVUQ",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T16:51:21.909200+00:00",
"file_format": "fastq",
"file_size": 5295214616,
"href": "/sequence-files/IGVFFI7929HVUQ/@@download/IGVFFI7929HVUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/e7a3af75-c8e9-47b8-b577-f792e3826c17/IGVFFI7929HVUQ.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-C38D5-Pos1-A11_S11_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6160UXFK/",
"accession": "IGVFFI6160UXFK",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T16:08:15.110248+00:00",
"file_format": "fastq",
"file_size": 5338016119,
"href": "/sequence-files/IGVFFI6160UXFK/@@download/IGVFFI6160UXFK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/5844de76-0766-45de-89aa-b75d50c68350/IGVFFI6160UXFK.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-C38D5-Pos1-A11_S11_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5043EYRM/",
"accession": "IGVFFI5043EYRM",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T14:25:38.272964+00:00",
"file_format": "fastq",
"file_size": 5318108317,
"href": "/sequence-files/IGVFFI5043EYRM/@@download/IGVFFI5043EYRM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/5d3f3f37-3080-47e3-9a6d-04b22257d109/IGVFFI5043EYRM.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-C38D5-Pos1-A11_S11_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9860QJDJ/",
"accession": "IGVFFI9860QJDJ",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T14:44:34.391969+00:00",
"file_format": "fastq",
"file_size": 5269603012,
"href": "/sequence-files/IGVFFI9860QJDJ/@@download/IGVFFI9860QJDJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/772f8e3a-b4fd-493d-a0eb-c7a01088ec82/IGVFFI9860QJDJ.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-C38D5-Pos1-A11_S11_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1096BKKU/",
"accession": "IGVFFI1096BKKU",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T15:07:03.889567+00:00",
"file_format": "fastq",
"file_size": 5233571931,
"href": "/sequence-files/IGVFFI1096BKKU/@@download/IGVFFI1096BKKU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/45051e05-138f-4fee-ac31-ed951ccf9736/IGVFFI1096BKKU.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-C38D5-Pos1-A11_S11_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9682HXQV/",
"accession": "IGVFFI9682HXQV",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T15:46:53.016737+00:00",
"file_format": "fastq",
"file_size": 5407287461,
"href": "/sequence-files/IGVFFI9682HXQV/@@download/IGVFFI9682HXQV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/bc622745-738c-40c1-8b6f-21014098b293/IGVFFI9682HXQV.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-C38D5-Pos1-A11_S11_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0754NCXT/",
"accession": "IGVFFI0754NCXT",
"aliases": [
"chongyuan-luo:pgp_snmct_C38_day5_L4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T16:29:17.568956+00:00",
"file_format": "fastq",
"file_size": 5383346660,
"href": "/sequence-files/IGVFFI0754NCXT/@@download/IGVFFI0754NCXT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/8e3cc2a2-b425-42bb-a530-6372c645090d/IGVFFI0754NCXT.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-C38D5-Pos1-A11_S11_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": "2025-02-11T00:54:23.165427+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1171PVMI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1171PVMI",
"aliases": [
"chongyuan-luo:C38_day5"
],
"classifications": [
"reprogrammed cell specimen"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/18b2e0b6-edec-475b-af8a-0afc04fa43d7/",
"certificate_identifier": "IP107-02",
"controlled_access": false,
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000057/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "fibroblast",
"term_name": "fibroblast"
}
],
"status": "released",
"summary": "Homo sapiens fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 5 days",
"targeted_sample_term": {
"@id": "/sample-terms/EFO_0004905/",
"status": "released",
"term_name": "induced pluripotent stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/ec46dfbd-fc11-419d-81e8-8ba82ffe6375/",
"title": "Terence Li"
},
"submitted_files_timestamp": "2024-11-16T14:25:38.272964+00:00",
"summary": "snMCT-seq",
"uuid": "3cc16366-bc5b-47fd-a3df-986140e5c003"
}