{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6281FISI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6281FISI",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0"
],
"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 sequence specification",
"detail": "Measurement set [IGVFDS6281FISI](/measurement-sets/IGVFDS6281FISI/) has sequence file(s): [IGVFFI8178LKUL](/sequence-files/IGVFFI8178LKUL/), [IGVFFI9059HREB](/sequence-files/IGVFFI9059HREB/), [IGVFFI3878BXYH](/sequence-files/IGVFFI3878BXYH/), [IGVFFI9159NQSU](/sequence-files/IGVFFI9159NQSU/), [IGVFFI8111UVWA](/sequence-files/IGVFFI8111UVWA/), [IGVFFI9614TMLA](/sequence-files/IGVFFI9614TMLA/), [IGVFFI9219PAZY](/sequence-files/IGVFFI9219PAZY/), [IGVFFI4045DXXJ](/sequence-files/IGVFFI4045DXXJ/) 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/IGVFDS6281FISI/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS6281FISI](/measurement-sets/IGVFDS6281FISI/) 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/IGVFDS6281FISI/"
}
]
},
"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": "2024-11-15T19:28:33.421241+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0351NYZH/",
"accession": "IGVFDO0351NYZH",
"aliases": [
"chongyuan-luo:C37"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8178LKUL/",
"accession": "IGVFFI8178LKUL",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:38:26.906676+00:00",
"file_format": "fastq",
"file_size": 5952069662,
"href": "/sequence-files/IGVFFI8178LKUL/@@download/IGVFFI8178LKUL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/08236dda-792c-4697-85db-ee58482894da/IGVFFI8178LKUL.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-C37D0-Pos1-C01_S25_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9059HREB/",
"accession": "IGVFFI9059HREB",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:19:58.151442+00:00",
"file_format": "fastq",
"file_size": 5807946394,
"href": "/sequence-files/IGVFFI9059HREB/@@download/IGVFFI9059HREB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/63125993-cad3-4ba9-a284-32a4138d9346/IGVFFI9059HREB.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-C37D0-Pos1-C01_S25_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3878BXYH/",
"accession": "IGVFFI3878BXYH",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:26:59.356642+00:00",
"file_format": "fastq",
"file_size": 5675779321,
"href": "/sequence-files/IGVFFI3878BXYH/@@download/IGVFFI3878BXYH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/2538353d-4518-4bec-bc25-c57be4498aed/IGVFFI3878BXYH.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-C37D0-Pos1-C01_S25_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9159NQSU/",
"accession": "IGVFFI9159NQSU",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:31:09.816162+00:00",
"file_format": "fastq",
"file_size": 5771812403,
"href": "/sequence-files/IGVFFI9159NQSU/@@download/IGVFFI9159NQSU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/09cb321d-d5b5-49e3-901d-3a02f1f7e3c3/IGVFFI9159NQSU.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-C37D0-Pos1-C01_S25_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8111UVWA/",
"accession": "IGVFFI8111UVWA",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:34:30.817587+00:00",
"file_format": "fastq",
"file_size": 5913623810,
"href": "/sequence-files/IGVFFI8111UVWA/@@download/IGVFFI8111UVWA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/0e912d51-6290-4eac-b78c-59488dda93eb/IGVFFI8111UVWA.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-C37D0-Pos1-C01_S25_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9614TMLA/",
"accession": "IGVFFI9614TMLA",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:42:00.664865+00:00",
"file_format": "fastq",
"file_size": 5902072941,
"href": "/sequence-files/IGVFFI9614TMLA/@@download/IGVFFI9614TMLA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/2978c689-300c-415a-907b-e3be3ab5af28/IGVFFI9614TMLA.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-C37D0-Pos1-C01_S25_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9219PAZY/",
"accession": "IGVFFI9219PAZY",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:23:37.914349+00:00",
"file_format": "fastq",
"file_size": 5868261771,
"href": "/sequence-files/IGVFFI9219PAZY/@@download/IGVFFI9219PAZY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/4c3b8c1d-96ff-4a71-9e1d-ca0469bee0f2/IGVFFI9219PAZY.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-C37D0-Pos1-C01_S25_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4045DXXJ/",
"accession": "IGVFFI4045DXXJ",
"aliases": [
"chongyuan-luo:pgp_snmct_C37_day0_L4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-15T23:46:04.897450+00:00",
"file_format": "fastq",
"file_size": 5916338130,
"href": "/sequence-files/IGVFFI4045DXXJ/@@download/IGVFFI4045DXXJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/15/13ee96eb-78d3-4d7a-b9c7-4f48bc2a26bc/IGVFFI4045DXXJ.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-C37D0-Pos1-C01_S25_L004_R2_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": "2025-02-11T00:55:00.196229+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9498BCKY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9498BCKY",
"aliases": [
"chongyuan-luo:C37_day0"
],
"classifications": [
"cell line"
],
"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": "fibroblast cell line, Homo sapiens",
"taxa": "Homo sapiens"
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/ec46dfbd-fc11-419d-81e8-8ba82ffe6375/",
"title": "Terence Li"
},
"submitted_files_timestamp": "2024-11-15T23:19:58.151442+00:00",
"summary": "snMCT-seq",
"uuid": "194e0338-45f6-46b7-8548-22efe8d7dd3b"
}