{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6121CBDQ",
"aliases": [
"ansuman-satpathy:igvf11_analysis_set_10x4"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0153FJWJ](/matrix-files/IGVFFI0153FJWJ/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0153FJWJ/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0153FJWJ](/matrix-files/IGVFFI0153FJWJ/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0153FJWJ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8200CKYL](/multiplexed-samples/IGVFSM8200CKYL/) 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/IGVFSM8200CKYL/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS6121CBDQ](/analysis-sets/IGVFDS6121CBDQ/) has `input_file_sets` with multiplexed samples: [IGVFSM8200CKYL](/multiplexed-samples/IGVFSM8200CKYL/) 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/IGVFDS6121CBDQ/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS6121CBDQ](/analysis-sets/IGVFDS6121CBDQ/) 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/IGVFDS6121CBDQ/"
}
]
},
"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": "2025-03-21T23:04:49.310065+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/IGVFDO7411YYYE/",
"accession": "IGVFDO7411YYYE",
"aliases": [
"igvf:donor_of_h7"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI5550IBSN/",
"accession": "IGVFFI5550IBSN",
"aliases": [
"ansuman-satpathy:igvf11_fragments_10x4"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:09:06.805772+00:00",
"file_format": "tsv",
"file_size": 3617611116,
"href": "/tabular-files/IGVFFI5550IBSN/@@download/IGVFFI5550IBSN.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/2b2435ba-8d94-4881-9b3d-307612d89645/IGVFFI5550IBSN.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l4_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI0153FJWJ/",
"accession": "IGVFFI0153FJWJ",
"aliases": [
"ansuman-satpathy:igvf11_raw_rna_counts_10x4"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:06:45.948153+00:00",
"file_format": "hdf5",
"file_size": 143424018,
"href": "/matrix-files/IGVFFI0153FJWJ/@@download/IGVFFI0153FJWJ.h5",
"s3_uri": "s3://igvf-files/2025/01/28/61844030-97bf-4dd8-9df1-95e3be035644/IGVFFI0153FJWJ.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l4_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI9936KULB/",
"accession": "IGVFFI9936KULB",
"aliases": [
"ansuman-satpathy:igvf11_fragments_index_10x4"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:34.478778+00:00",
"file_format": "tbi",
"file_size": 1417512,
"href": "/index-files/IGVFFI9936KULB/@@download/IGVFFI9936KULB.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/acf1f768-6c2e-4a15-8716-80a5f2728a94/IGVFFI9936KULB.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l4_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2281SYIO/",
"accession": "IGVFFI2281SYIO",
"aliases": [
"ansuman-satpathy:igvf11_multiseq_count_matrix_10x4"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:32:54.327819+00:00",
"file_format": "tsv",
"file_size": 230714,
"href": "/tabular-files/IGVFFI2281SYIO/@@download/IGVFFI2281SYIO.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/99749397-1814-41bf-9cd3-f3e5fb0e4e1c/IGVFFI2281SYIO.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e11l4_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8715YPRJ/",
"accession": "IGVFFI8715YPRJ",
"aliases": [
"ansuman-satpathy:igvf11_peaks_10x4"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:09:30.879181+00:00",
"file_format": "bed",
"file_size": 1979532,
"href": "/tabular-files/IGVFFI8715YPRJ/@@download/IGVFFI8715YPRJ.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/3bc9d959-bc2f-45cd-aa64-3a3f878b2ca3/IGVFFI8715YPRJ.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l4_peaks.bed",
"upload_status": "validation exempted"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6138PRFG/",
"accession": "IGVFDS6138PRFG",
"aliases": [
"ansuman-satpathy:multiseq_igvf11_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6943MGVC/",
"accession": "IGVFDS6943MGVC",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf11_10x4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1824DNGD/",
"accession": "IGVFDS1824DNGD",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf11_10x4"
],
"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": "2025-03-22T00:43:06.619653+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11), H7-hESC",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8200CKYL/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8200CKYL",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf11_10x4"
],
"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"
},
{
"@id": "/institutional-certificates/f37dfa73-f4f1-4bfe-a312-9eade62d5988/",
"certificate_identifier": "IP115-15",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0005904/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H7-hESC"
],
"status": "released",
"summary": "H7-hESC",
"term_name": "H7-hESC"
},
{
"@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) H7-hESC differentiated cell specimen; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 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": "2025-01-28T06:09:06.805772+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "7f42b93e-3298-43aa-a998-b9b9ae257ddb",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}