{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4147ORMU/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4147ORMU",
"aliases": [
"ansuman-satpathy:igvf3_analysis_set_10x3"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4147ORMU](/analysis-sets/IGVFDS4147ORMU/) has `input_file_sets` with multiplexed samples: [IGVFSM7454SJSO](/multiplexed-samples/IGVFSM7454SJSO/) 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/IGVFDS4147ORMU/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4147ORMU](/analysis-sets/IGVFDS4147ORMU/) 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/IGVFDS4147ORMU/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7454SJSO](/multiplexed-samples/IGVFSM7454SJSO/) 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/IGVFSM7454SJSO/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI5603RZNN](/matrix-files/IGVFFI5603RZNN/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI5603RZNN/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI5603RZNN](/matrix-files/IGVFFI5603RZNN/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI5603RZNN/"
}
]
},
"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": "2025-03-21T23:04:30.709043+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2837BRET/",
"accession": "IGVFDO2837BRET",
"aliases": [
"igvf:donor_of_HepG2"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/index-files/IGVFFI1147RWJV/",
"accession": "IGVFFI1147RWJV",
"aliases": [
"ansuman-satpathy:igvf3_fragments_index_10x3"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:27:58.777572+00:00",
"file_format": "tbi",
"file_size": 1311120,
"href": "/index-files/IGVFFI1147RWJV/@@download/IGVFFI1147RWJV.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/b39a4308-0853-4a2c-9558-ffeb5582abb5/IGVFFI1147RWJV.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l3_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7589YNTD/",
"accession": "IGVFFI7589YNTD",
"aliases": [
"ansuman-satpathy:igvf3_fragments_10x3"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:51:27.757661+00:00",
"file_format": "tsv",
"file_size": 3112162324,
"href": "/tabular-files/IGVFFI7589YNTD/@@download/IGVFFI7589YNTD.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/2dd0e701-caab-45da-8ee3-37cadfd9cc26/IGVFFI7589YNTD.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l3_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI7181BPSL/",
"accession": "IGVFFI7181BPSL",
"aliases": [
"ansuman-satpathy:igvf3_multiseq_count_matrix_10x3"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:30:19.282830+00:00",
"file_format": "tsv",
"file_size": 284439,
"href": "/tabular-files/IGVFFI7181BPSL/@@download/IGVFFI7181BPSL.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/dbc53c9a-df2d-4484-831c-c09506979690/IGVFFI7181BPSL.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e3l3_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8832FBGF/",
"accession": "IGVFFI8832FBGF",
"aliases": [
"ansuman-satpathy:igvf3_peaks_10x3"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:51:46.091052+00:00",
"file_format": "bed",
"file_size": 2053793,
"href": "/tabular-files/IGVFFI8832FBGF/@@download/IGVFFI8832FBGF.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/22755f4b-d126-4c6c-9ddd-5477afb73453/IGVFFI8832FBGF.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l3_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI5603RZNN/",
"accession": "IGVFFI5603RZNN",
"aliases": [
"ansuman-satpathy:igvf3_raw_rna_counts_10x3"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:34:31.741360+00:00",
"file_format": "hdf5",
"file_size": 90400932,
"href": "/matrix-files/IGVFFI5603RZNN/@@download/IGVFFI5603RZNN.h5",
"s3_uri": "s3://igvf-files/2025/01/28/2b2e216e-0b35-44ca-87c0-ec7815cd10b9/IGVFFI5603RZNN.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l3_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5693MIIK/",
"accession": "IGVFDS5693MIIK",
"aliases": [
"ansuman-satpathy:multiseq_igvf3_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1983YORK/",
"accession": "IGVFDS1983YORK",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf3_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1843ABDU/",
"accession": "IGVFDS1843ABDU",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf3_10x3"
],
"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": "2025-03-22T00:42:21.873127+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11), H9, HepG2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7454SJSO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7454SJSO",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf3_10x3"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/90b62a08-60dc-4932-8bf1-38769f07b362/",
"certificate_identifier": "IP115-06",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
"certificate_identifier": "IP115-21",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/eaf8c672-701d-4aee-9108-8d64c472d20e/",
"certificate_identifier": "IP115-14",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001187/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HepG2"
],
"status": "released",
"summary": "HepG2",
"term_name": "HepG2"
},
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
},
{
"@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 (female) H9 differentiated cell specimen induced to cardiac muscle cell for 15 days; Homo sapiens (male) HepG2 cell line grown in DMEM without serum; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T05:51:27.757661+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "8101880e-0f06-4636-b59e-730e193fb316",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}