{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6039JXBR",
"aliases": [
"ansuman-satpathy:igvf15_analysis_set",
"ansuman-satpathy:igvf15_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS6039JXBR](/analysis-sets/IGVFDS6039JXBR/) has `input_file_sets` with multiplexed samples: [IGVFSM2174QALS](/multiplexed-samples/IGVFSM2174QALS/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_analysis_set_multiplexed_samples",
"path": "/analysis-sets/IGVFDS6039JXBR/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS6039JXBR](/analysis-sets/IGVFDS6039JXBR/) 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": "/analysis-sets/IGVFDS6039JXBR/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM2174QALS](/multiplexed-samples/IGVFSM2174QALS/) 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": "/multiplexed-samples/IGVFSM2174QALS/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:34:56.935296+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - WTC11 hepatocyte differentiation",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
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"accession": "IGVFFI7132ZSRN",
"aliases": [
"ansuman-satpathy:igvf15_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:27:31.634042+00:00",
"derived_from": [
"/sequence-files/IGVFFI2853SSND/",
"/sequence-files/IGVFFI5766MIHS/",
"/sequence-files/IGVFFI3692BTHU/",
"/sequence-files/IGVFFI7380SYVV/",
"/sequence-files/IGVFFI3057TBTI/",
"/sequence-files/IGVFFI4855ASAI/",
"/sequence-files/IGVFFI8321JOIP/",
"/sequence-files/IGVFFI2599QHOU/"
],
"file_format": "tsv",
"file_size": 4655981930,
"href": "/tabular-files/IGVFFI7132ZSRN/@@download/IGVFFI7132ZSRN.tsv.gz",
"md5sum": "0860e3fa525e1ee0170ece8232595e76",
"s3_uri": "s3://igvf-files/2025/01/28/cf637ab9-d60f-40c2-95c8-0bda3d7326dd/IGVFFI7132ZSRN.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI1443DGBS/",
"accession": "IGVFFI1443DGBS",
"aliases": [
"ansuman-satpathy:igvf15_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:27:57.668693+00:00",
"derived_from": [
"/tabular-files/IGVFFI7132ZSRN/"
],
"file_format": "bed",
"file_size": 2699957,
"href": "/tabular-files/IGVFFI1443DGBS/@@download/IGVFFI1443DGBS.bed.gz",
"md5sum": "596525f87759383c34a1d1e1ed281782",
"s3_uri": "s3://igvf-files/2025/01/28/bd110c77-ed82-47af-a759-41b9eddee23c/IGVFFI1443DGBS.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI0525GPAQ/",
"accession": "IGVFFI0525GPAQ",
"aliases": [
"ansuman-satpathy:igvf15_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:15.381008+00:00",
"derived_from": [
"/tabular-files/IGVFFI7132ZSRN/"
],
"file_format": "tbi",
"file_size": 1622407,
"href": "/index-files/IGVFFI0525GPAQ/@@download/IGVFFI0525GPAQ.tbi",
"md5sum": "38eb5844e4126911589d1b3f9d50fa86",
"s3_uri": "s3://igvf-files/2025/01/28/ee90d5ee-f372-4753-8b67-4637b3b515f2/IGVFFI0525GPAQ.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI5378PZTF/",
"accession": "IGVFFI5378PZTF",
"aliases": [
"ansuman-satpathy:igvf15_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:10:37.648241+00:00",
"derived_from": [
"/sequence-files/IGVFFI7711ZJTT/",
"/sequence-files/IGVFFI8681HIWH/",
"/sequence-files/IGVFFI5859SOOF/",
"/sequence-files/IGVFFI3335AQLU/",
"/sequence-files/IGVFFI3835VFVF/",
"/sequence-files/IGVFFI1508WDYW/",
"/sequence-files/IGVFFI1830GJBO/",
"/sequence-files/IGVFFI4542ISGP/"
],
"file_format": "hdf5",
"file_size": 189027531,
"href": "/matrix-files/IGVFFI5378PZTF/@@download/IGVFFI5378PZTF.h5",
"md5sum": "74552320bb7a737191337f92b95ad0fc",
"s3_uri": "s3://igvf-files/2025/01/28/c6830ce2-03d4-4e77-8bf4-6b78624ad38c/IGVFFI5378PZTF.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1271TKWE/",
"accession": "IGVFFI1271TKWE",
"aliases": [
"ansuman-satpathy:igvf15_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:35:56.131399+00:00",
"derived_from": [
"/sequence-files/IGVFFI1084BWDO/",
"/sequence-files/IGVFFI4994MRYA/",
"/sequence-files/IGVFFI1587VJXD/",
"/sequence-files/IGVFFI9129UCYU/",
"/sequence-files/IGVFFI9835ATAB/",
"/sequence-files/IGVFFI0978AHIS/",
"/sequence-files/IGVFFI7829MAXE/",
"/sequence-files/IGVFFI7854UIQP/"
],
"file_format": "tsv",
"file_size": 875620,
"href": "/tabular-files/IGVFFI1271TKWE/@@download/IGVFFI1271TKWE.tsv.gz",
"md5sum": "0d22275a8148a4ef583180a6fd1fb84b",
"s3_uri": "s3://igvf-files/2025/02/19/c68d2de7-1c08-40c3-8a3b-a54c219aa653/IGVFFI1271TKWE.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e15l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2440YLWS/",
"accession": "IGVFDS2440YLWS",
"aliases": [
"ansuman-satpathy:multiseq_igvf15_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4338ZSWY/",
"accession": "IGVFDS4338ZSWY",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf15_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2623QODS/",
"accession": "IGVFDS2623QODS",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf15_10x1"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"release_timestamp": "2025-03-07T06:05:10.951221+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11)",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2174QALS/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2174QALS",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf15_10x1"
],
"cellular_sub_pool": "1",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
"certificate_identifier": "IP115-21",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to liver for 18 days; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to liver for 13 days; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T06:27:31.634042+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "c41a3b18-6225-411e-b555-eab84ca4d704",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}