{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3114UZXE",
"aliases": [
"ansuman-satpathy:igvf15_analysis_set_10x3"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI4195HOBE](/matrix-files/IGVFFI4195HOBE/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI4195HOBE/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI4195HOBE](/matrix-files/IGVFFI4195HOBE/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI4195HOBE/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS3114UZXE](/analysis-sets/IGVFDS3114UZXE/) has `input_file_sets` with multiplexed samples: [IGVFSM1624SZQN](/multiplexed-samples/IGVFSM1624SZQN/) 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/IGVFDS3114UZXE/"
}
]
},
"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": "2025-03-21T23:05:09.334595+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"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI4981LXWG/",
"accession": "IGVFFI4981LXWG",
"aliases": [
"ansuman-satpathy:igvf15_multiseq_count_matrix_10x3"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:36:07.817736+00:00",
"file_format": "tsv",
"file_size": 651319,
"href": "/tabular-files/IGVFFI4981LXWG/@@download/IGVFFI4981LXWG.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/61973923-0fbd-4fe0-b26f-4c0cf2de6c65/IGVFFI4981LXWG.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e15l3_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9118EYAP/",
"accession": "IGVFFI9118EYAP",
"aliases": [
"ansuman-satpathy:igvf15_fragments_10x3"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:28:59.927589+00:00",
"file_format": "tsv",
"file_size": 4667328825,
"href": "/tabular-files/IGVFFI9118EYAP/@@download/IGVFFI9118EYAP.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/bf6bfe7b-0d9e-4756-8483-26f7774ba128/IGVFFI9118EYAP.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l3_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI3604TINQ/",
"accession": "IGVFFI3604TINQ",
"aliases": [
"ansuman-satpathy:igvf15_fragments_index_10x3"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:17.676459+00:00",
"file_format": "tbi",
"file_size": 1626871,
"href": "/index-files/IGVFFI3604TINQ/@@download/IGVFFI3604TINQ.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/222eda97-40d0-4840-82d1-5c73246f68d9/IGVFFI3604TINQ.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l3_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1102UMNU/",
"accession": "IGVFFI1102UMNU",
"aliases": [
"ansuman-satpathy:igvf15_peaks_10x3"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:29:27.875629+00:00",
"file_format": "bed",
"file_size": 2661701,
"href": "/tabular-files/IGVFFI1102UMNU/@@download/IGVFFI1102UMNU.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/ad0e2a95-0f6d-4eb2-96fa-7a24df12871d/IGVFFI1102UMNU.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l3_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI4195HOBE/",
"accession": "IGVFFI4195HOBE",
"aliases": [
"ansuman-satpathy:igvf15_raw_rna_counts_10x3"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:10:56.693577+00:00",
"file_format": "hdf5",
"file_size": 181008580,
"href": "/matrix-files/IGVFFI4195HOBE/@@download/IGVFFI4195HOBE.h5",
"s3_uri": "s3://igvf-files/2025/01/28/ad7333b9-f652-4340-973f-c4df44beb7a6/IGVFFI4195HOBE.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf15/e15l3_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8920TKBO/",
"accession": "IGVFDS8920TKBO",
"aliases": [
"ansuman-satpathy:multiseq_igvf15_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8563NWFI/",
"accession": "IGVFDS8563NWFI",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf15_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8608TBPZ/",
"accession": "IGVFDS8608TBPZ",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf15_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": "2025-03-22T00:44:10.686950+00:00",
"sample_summary": "multiplexed sample of GM25256 (WTC-11)",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM1624SZQN/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1624SZQN",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf15_10x3"
],
"cellular_sub_pool": "3",
"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/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T06:28:59.927589+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "e5a5891f-0da2-4e64-873f-4a309ac6c4c6",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}