{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9196PDRB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9196PDRB",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9"
],
"assay_term": {
"@id": "/assay-terms/NTR_0000745/",
"assay_slims": [
"multiome"
],
"status": "released",
"term_name": "single nucleus methylation and chromatin conformation capture sequencing"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9196PDRB](/measurement-sets/IGVFDS9196PDRB/) has sequence file(s): [IGVFFI4058NAXU](/sequence-files/IGVFFI4058NAXU/), [IGVFFI2481VZHT](/sequence-files/IGVFFI2481VZHT/), [IGVFFI9488BLRX](/sequence-files/IGVFFI9488BLRX/), [IGVFFI9216KLOV](/sequence-files/IGVFFI9216KLOV/), [IGVFFI5897TTFO](/sequence-files/IGVFFI5897TTFO/), [IGVFFI7196VYNX](/sequence-files/IGVFFI7196VYNX/), [IGVFFI9478IFDS](/sequence-files/IGVFFI9478IFDS/), [IGVFFI7429JLVG](/sequence-files/IGVFFI7429JLVG/), [IGVFFI4042QBZQ](/sequence-files/IGVFFI4042QBZQ/), [IGVFFI2424JMXS](/sequence-files/IGVFFI2424JMXS/), [IGVFFI7682ELAV](/sequence-files/IGVFFI7682ELAV/), [IGVFFI2281JWJS](/sequence-files/IGVFFI2281JWJS/), [IGVFFI0405YMON](/sequence-files/IGVFFI0405YMON/), [IGVFFI0575PBZP](/sequence-files/IGVFFI0575PBZP/), [IGVFFI2054TJPO](/sequence-files/IGVFFI2054TJPO/), [IGVFFI1036VXVV](/sequence-files/IGVFFI1036VXVV/) 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/IGVFDS9196PDRB/"
},
{
"category": "NTR term ID",
"detail": "Assay term for [NTR_0000745](/assay-terms/NTR_0000745/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/assay-terms/NTR_0000745/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS9196PDRB](/measurement-sets/IGVFDS9196PDRB/) 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/IGVFDS9196PDRB/"
}
]
},
"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": "2024-11-15T19:29:26.689967+00:00",
"donors": [
{
"@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/IGVFFI4058NAXU/",
"accession": "IGVFFI4058NAXU",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T00:50:20.198084+00:00",
"file_format": "fastq",
"file_size": 3487485562,
"href": "/sequence-files/IGVFFI4058NAXU/@@download/IGVFFI4058NAXU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/9da17c56-ab29-499a-9e2c-03b7eca328cf/IGVFFI4058NAXU.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2481VZHT/",
"accession": "IGVFFI2481VZHT",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T01:35:07.969697+00:00",
"file_format": "fastq",
"file_size": 3530010366,
"href": "/sequence-files/IGVFFI2481VZHT/@@download/IGVFFI2481VZHT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/ac047afe-2a33-4383-964a-c4e1ed75732a/IGVFFI2481VZHT.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9488BLRX/",
"accession": "IGVFFI9488BLRX",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-17T23:09:23.175230+00:00",
"file_format": "fastq",
"file_size": 3323022524,
"href": "/sequence-files/IGVFFI9488BLRX/@@download/IGVFFI9488BLRX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/17/ea2221e1-1737-4c2c-bf92-3b6476718158/IGVFFI9488BLRX.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9216KLOV/",
"accession": "IGVFFI9216KLOV",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-17T23:50:37.392434+00:00",
"file_format": "fastq",
"file_size": 3446988649,
"href": "/sequence-files/IGVFFI9216KLOV/@@download/IGVFFI9216KLOV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/17/9104bee2-89a6-48bd-8f15-c33cde9430e0/IGVFFI9216KLOV.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5897TTFO/",
"accession": "IGVFFI5897TTFO",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T01:05:08.104990+00:00",
"file_format": "fastq",
"file_size": 3576811102,
"href": "/sequence-files/IGVFFI5897TTFO/@@download/IGVFFI5897TTFO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/8f8d8837-3c5a-4d8d-9d58-817cd8d32c6a/IGVFFI5897TTFO.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7196VYNX/",
"accession": "IGVFFI7196VYNX",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-17T23:37:46.273889+00:00",
"file_format": "fastq",
"file_size": 3496259248,
"href": "/sequence-files/IGVFFI7196VYNX/@@download/IGVFFI7196VYNX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/17/74f7ec9c-d4fc-4224-8e2e-74110ce327e9/IGVFFI7196VYNX.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9478IFDS/",
"accession": "IGVFFI9478IFDS",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T00:35:20.650372+00:00",
"file_format": "fastq",
"file_size": 3542664039,
"href": "/sequence-files/IGVFFI9478IFDS/@@download/IGVFFI9478IFDS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/d09f0cf8-83ef-4e3f-93e4-c330a181f9d4/IGVFFI9478IFDS.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7429JLVG/",
"accession": "IGVFFI7429JLVG",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T00:05:12.500288+00:00",
"file_format": "fastq",
"file_size": 3534081428,
"href": "/sequence-files/IGVFFI7429JLVG/@@download/IGVFFI7429JLVG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/6c656957-3c04-4e23-ab2e-f1661baaf2c2/IGVFFI7429JLVG.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4042QBZQ/",
"accession": "IGVFFI4042QBZQ",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-17T23:22:34.547833+00:00",
"file_format": "fastq",
"file_size": 3409021529,
"href": "/sequence-files/IGVFFI4042QBZQ/@@download/IGVFFI4042QBZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/17/7da038de-7b49-447f-b02e-aa6521bde63d/IGVFFI4042QBZQ.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2424JMXS/",
"accession": "IGVFFI2424JMXS",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-17T22:56:17.725381+00:00",
"file_format": "fastq",
"file_size": 3266626408,
"href": "/sequence-files/IGVFFI2424JMXS/@@download/IGVFFI2424JMXS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/17/b7d403d2-0c5f-471b-8122-4a5312f6ecdc/IGVFFI2424JMXS.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7682ELAV/",
"accession": "IGVFFI7682ELAV",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T00:20:20.653631+00:00",
"file_format": "fastq",
"file_size": 3475739633,
"href": "/sequence-files/IGVFFI7682ELAV/@@download/IGVFFI7682ELAV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/9ccbe42a-1281-4e93-8f6a-50173d689ced/IGVFFI7682ELAV.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2281JWJS/",
"accession": "IGVFFI2281JWJS",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T01:50:10.136290+00:00",
"file_format": "fastq",
"file_size": 3429017978,
"href": "/sequence-files/IGVFFI2281JWJS/@@download/IGVFFI2281JWJS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/cf378d52-e54c-40f0-bf27-9e821a3087c6/IGVFFI2281JWJS.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0405YMON/",
"accession": "IGVFFI0405YMON",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T02:05:15.147237+00:00",
"file_format": "fastq",
"file_size": 3518182079,
"href": "/sequence-files/IGVFFI0405YMON/@@download/IGVFFI0405YMON.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/99123464-9a70-4e77-927b-82b67b7ddd03/IGVFFI0405YMON.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0575PBZP/",
"accession": "IGVFFI0575PBZP",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T01:20:25.276453+00:00",
"file_format": "fastq",
"file_size": 3451734344,
"href": "/sequence-files/IGVFFI0575PBZP/@@download/IGVFFI0575PBZP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/a725127a-619a-4cdb-9e89-6c374f56d5ea/IGVFFI0575PBZP.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2054TJPO/",
"accession": "IGVFFI2054TJPO",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T02:20:10.512580+00:00",
"file_format": "fastq",
"file_size": 3313476310,
"href": "/sequence-files/IGVFFI2054TJPO/@@download/IGVFFI2054TJPO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/445dc713-31e4-478b-a50f-7a86159fccf1/IGVFFI2054TJPO.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1036VXVV/",
"accession": "IGVFFI1036VXVV",
"aliases": [
"chongyuan-luo:pgp_snm3c_C39_day9_L8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-18T02:34:47.549349+00:00",
"file_format": "fastq",
"file_size": 3372459599,
"href": "/sequence-files/IGVFFI1036VXVV/@@download/IGVFFI1036VXVV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/18/355c2aed-2df6-47db-aea8-21287026b165/IGVFFI1036VXVV.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/snm3c/yzcl47/20231005-3C39D9-Pos1-C09_S30_L008_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/chongyuan-luo/",
"title": "Chongyuan Luo, UCLA"
},
"preferred_assay_title": "snM3C-seq",
"protocols": [
"https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1"
],
"release_timestamp": "2025-02-11T00:54:51.242313+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3665LIKW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3665LIKW",
"aliases": [
"chongyuan-luo:C39_day9"
],
"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": "fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 9 days, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/EFO_0004905/",
"status": "released",
"term_name": "induced pluripotent stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/ec46dfbd-fc11-419d-81e8-8ba82ffe6375/",
"title": "Terence Li"
},
"submitted_files_timestamp": "2024-11-17T22:56:17.725381+00:00",
"summary": "snM3C-seq",
"uuid": "592dad57-e156-4644-b4fb-543cbe3e49de"
}