{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9131TLJM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9131TLJM",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16"
],
"assay_term": {
"@id": "/assay-terms/NTR_0000745/",
"status": "released",
"term_name": "single nucleus methylation and chromatin conformation capture sequencing"
},
"audit": {
"INTERNAL_ACTION": [
{
"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/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9131TLJM](/measurement-sets/IGVFDS9131TLJM/) has sequence file(s): [IGVFFI9754SOQX](/sequence-files/IGVFFI9754SOQX/), [IGVFFI0121ADAO](/sequence-files/IGVFFI0121ADAO/), [IGVFFI2308ICAY](/sequence-files/IGVFFI2308ICAY/), [IGVFFI2906IZMA](/sequence-files/IGVFFI2906IZMA/), [IGVFFI6106FCKT](/sequence-files/IGVFFI6106FCKT/), [IGVFFI5438FMTK](/sequence-files/IGVFFI5438FMTK/), [IGVFFI2145XVYA](/sequence-files/IGVFFI2145XVYA/), [IGVFFI0574OWGQ](/sequence-files/IGVFFI0574OWGQ/), [IGVFFI2883GWAE](/sequence-files/IGVFFI2883GWAE/), [IGVFFI5984WPOK](/sequence-files/IGVFFI5984WPOK/), [IGVFFI6051UOKG](/sequence-files/IGVFFI6051UOKG/), [IGVFFI3386WNUY](/sequence-files/IGVFFI3386WNUY/), [IGVFFI4622ZWOT](/sequence-files/IGVFFI4622ZWOT/), [IGVFFI1853HSMD](/sequence-files/IGVFFI1853HSMD/), [IGVFFI3765NKCZ](/sequence-files/IGVFFI3765NKCZ/), [IGVFFI9177KBRA](/sequence-files/IGVFFI9177KBRA/) 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/IGVFDS9131TLJM/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS9131TLJM](/measurement-sets/IGVFDS9131TLJM/) 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/IGVFDS9131TLJM/"
}
]
},
"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": "2024-11-15T19:29:19.864175+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/IGVFFI9754SOQX/",
"accession": "IGVFFI9754SOQX",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T07:30:43.174619+00:00",
"file_format": "fastq",
"file_size": 2841316506,
"href": "/sequence-files/IGVFFI9754SOQX/@@download/IGVFFI9754SOQX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/a611c86d-2cfb-4fd2-819a-0f645bbab91a/IGVFFI9754SOQX.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0121ADAO/",
"accession": "IGVFFI0121ADAO",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T07:43:33.520586+00:00",
"file_format": "fastq",
"file_size": 2908250692,
"href": "/sequence-files/IGVFFI0121ADAO/@@download/IGVFFI0121ADAO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/a98debb9-90d6-45b5-ba25-3937b5db591a/IGVFFI0121ADAO.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2308ICAY/",
"accession": "IGVFFI2308ICAY",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T08:10:00.892702+00:00",
"file_format": "fastq",
"file_size": 2937383636,
"href": "/sequence-files/IGVFFI2308ICAY/@@download/IGVFFI2308ICAY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/d09791a8-2795-42df-baff-bed8ead2f850/IGVFFI2308ICAY.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2906IZMA/",
"accession": "IGVFFI2906IZMA",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T08:23:32.627842+00:00",
"file_format": "fastq",
"file_size": 2886420314,
"href": "/sequence-files/IGVFFI2906IZMA/@@download/IGVFFI2906IZMA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/ba2cf3e6-cfad-4635-ad3e-d2b547c04795/IGVFFI2906IZMA.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6106FCKT/",
"accession": "IGVFFI6106FCKT",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T08:35:34.938013+00:00",
"file_format": "fastq",
"file_size": 2936670728,
"href": "/sequence-files/IGVFFI6106FCKT/@@download/IGVFFI6106FCKT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/e6015364-2aa6-4117-a756-92b5cfe7bcb2/IGVFFI6106FCKT.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5438FMTK/",
"accession": "IGVFFI5438FMTK",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T08:49:36.741259+00:00",
"file_format": "fastq",
"file_size": 2897617013,
"href": "/sequence-files/IGVFFI5438FMTK/@@download/IGVFFI5438FMTK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/4c0fe68a-954c-4bf6-8eff-7ed0c7ee949c/IGVFFI5438FMTK.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2145XVYA/",
"accession": "IGVFFI2145XVYA",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T09:25:21.511030+00:00",
"file_format": "fastq",
"file_size": 2936070102,
"href": "/sequence-files/IGVFFI2145XVYA/@@download/IGVFFI2145XVYA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/8aa43a16-d3ac-4edc-b552-6e3af2529c99/IGVFFI2145XVYA.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0574OWGQ/",
"accession": "IGVFFI0574OWGQ",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T09:50:47.954820+00:00",
"file_format": "fastq",
"file_size": 2922998979,
"href": "/sequence-files/IGVFFI0574OWGQ/@@download/IGVFFI0574OWGQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/01c5152c-42e4-46d5-a74f-ae01710dd235/IGVFFI0574OWGQ.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2883GWAE/",
"accession": "IGVFFI2883GWAE",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T09:14:25.571995+00:00",
"file_format": "fastq",
"file_size": 2876270308,
"href": "/sequence-files/IGVFFI2883GWAE/@@download/IGVFFI2883GWAE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/1d43cb46-1286-4422-a364-5788fcc20232/IGVFFI2883GWAE.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5984WPOK/",
"accession": "IGVFFI5984WPOK",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T07:06:47.789520+00:00",
"file_format": "fastq",
"file_size": 2739075758,
"href": "/sequence-files/IGVFFI5984WPOK/@@download/IGVFFI5984WPOK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/c2e2773c-9355-4467-9547-32c09b6f8d05/IGVFFI5984WPOK.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6051UOKG/",
"accession": "IGVFFI6051UOKG",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T07:19:27.229274+00:00",
"file_format": "fastq",
"file_size": 2781120037,
"href": "/sequence-files/IGVFFI6051UOKG/@@download/IGVFFI6051UOKG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/318b0009-8ee7-4574-8172-09b44e33c95c/IGVFFI6051UOKG.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3386WNUY/",
"accession": "IGVFFI3386WNUY",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T07:56:35.144249+00:00",
"file_format": "fastq",
"file_size": 2870221199,
"href": "/sequence-files/IGVFFI3386WNUY/@@download/IGVFFI3386WNUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/1f03485b-1480-4135-8de2-e291085d7963/IGVFFI3386WNUY.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4622ZWOT/",
"accession": "IGVFFI4622ZWOT",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T09:00:21.776052+00:00",
"file_format": "fastq",
"file_size": 2967395883,
"href": "/sequence-files/IGVFFI4622ZWOT/@@download/IGVFFI4622ZWOT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/fb07b04a-e353-4c1e-b331-26e204365b64/IGVFFI4622ZWOT.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1853HSMD/",
"accession": "IGVFFI1853HSMD",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T10:15:30.266204+00:00",
"file_format": "fastq",
"file_size": 2822373745,
"href": "/sequence-files/IGVFFI1853HSMD/@@download/IGVFFI1853HSMD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/cb3f4136-0d1c-4311-8f97-d4d0a66a7ec3/IGVFFI1853HSMD.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3765NKCZ/",
"accession": "IGVFFI3765NKCZ",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T09:38:47.030970+00:00",
"file_format": "fastq",
"file_size": 2854932777,
"href": "/sequence-files/IGVFFI3765NKCZ/@@download/IGVFFI3765NKCZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/6536ecad-a882-4dab-a2b5-7abaa6f55b23/IGVFFI3765NKCZ.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9177KBRA/",
"accession": "IGVFFI9177KBRA",
"aliases": [
"chongyuan-luo:pgp_snm3c_C29_day16_L8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-16T10:03:47.510786+00:00",
"file_format": "fastq",
"file_size": 2780642245,
"href": "/sequence-files/IGVFFI9177KBRA/@@download/IGVFFI9177KBRA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/16/94d41e52-7499-4ffd-873a-e328932b6a4f/IGVFFI9177KBRA.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/yzcl47/20231005-3C29D16-Pos1-B01_S11_L008_R1_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": "2025-02-11T00:54:41.547947+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9359NPEE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9359NPEE",
"aliases": [
"chongyuan-luo:C29_day16"
],
"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 16 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": "2024-11-16T07:06:47.789520+00:00",
"summary": "snM3C-seq",
"uuid": "935e701f-74c5-4474-bb6f-8cb9307bd5ac"
}