{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5901DVUG/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5901DVUG",
"aliases": [
"ansuman-satpathy:igvf13_analysis_set",
"ansuman-satpathy:igvf13_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM6422YWWA](/multiplexed-samples/IGVFSM6422YWWA/) has in progress subobject tabular file [IGVFFI7218IPWP](/tabular-files/IGVFFI7218IPWP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM6422YWWA/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM6422YWWA](/multiplexed-samples/IGVFSM6422YWWA/) 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/IGVFSM6422YWWA/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI1298VEUV](/matrix-files/IGVFFI1298VEUV/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI1298VEUV/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI1298VEUV](/matrix-files/IGVFFI1298VEUV/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI1298VEUV/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS5901DVUG](/analysis-sets/IGVFDS5901DVUG/) has `input_file_sets` with multiplexed samples: [IGVFSM6422YWWA](/multiplexed-samples/IGVFSM6422YWWA/) 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/IGVFDS5901DVUG/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS5901DVUG](/analysis-sets/IGVFDS5901DVUG/) 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/IGVFDS5901DVUG/"
}
]
},
"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": true,
"creation_timestamp": "2025-01-28T05:34:55.277668+00:00",
"data_use_limitation_summaries": [
"GRU-PUB"
],
"description": "Quality-control workflow performed by Satpathy Lab - Human coronary artery",
"donors": [
{
"@id": "/human-donors/IGVFDO2120EMSK/",
"accession": "IGVFDO2120EMSK",
"aliases": [
"thomas-quertermous:LAD_multiome_donor1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4556QZMA/",
"accession": "IGVFDO4556QZMA",
"aliases": [
"thomas-quertermous:LAD_multiome_donor4"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1255NCVH/",
"accession": "IGVFDO1255NCVH",
"aliases": [
"thomas-quertermous:LAD_multiome_donor2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4204VAPA/",
"accession": "IGVFDO4204VAPA",
"aliases": [
"thomas-quertermous:LAD_multiome_donor3"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI9273HUJF/",
"accession": "IGVFFI9273HUJF",
"aliases": [
"ansuman-satpathy:igvf13_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:23:50.616112+00:00",
"file_format": "bed",
"file_size": 728366,
"href": "/tabular-files/IGVFFI9273HUJF/@@download/IGVFFI9273HUJF.bed.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/714b73a7-7a6c-4731-8b8d-224402d867d4/IGVFFI9273HUJF.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI3092VBKJ/",
"accession": "IGVFFI3092VBKJ",
"aliases": [
"ansuman-satpathy:igvf13_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:23:16.240916+00:00",
"file_format": "tsv",
"file_size": 5327641058,
"href": "/tabular-files/IGVFFI3092VBKJ/@@download/IGVFFI3092VBKJ.tsv.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/eacb87f8-bb2e-41c6-b518-3f0405806c92/IGVFFI3092VBKJ.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI0641CLXM/",
"accession": "IGVFFI0641CLXM",
"aliases": [
"ansuman-satpathy:igvf13_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": true,
"creation_timestamp": "2025-01-28T15:29:08.169569+00:00",
"file_format": "tbi",
"file_size": 1564813,
"href": "/index-files/IGVFFI0641CLXM/@@download/IGVFFI0641CLXM.tbi",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/780b1011-481c-4b1b-b091-8b532e3b6f03/IGVFFI0641CLXM.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI1298VEUV/",
"accession": "IGVFFI1298VEUV",
"aliases": [
"ansuman-satpathy:igvf13_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:09:53.920723+00:00",
"file_format": "hdf5",
"file_size": 130657456,
"href": "/matrix-files/IGVFFI1298VEUV/@@download/IGVFFI1298VEUV.h5",
"s3_uri": "s3://igvf-files/2025/01/28/3c77d232-f24b-4ae5-8227-1e50afe0e6ce/IGVFFI1298VEUV.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1470AONX/",
"accession": "IGVFFI1470AONX",
"aliases": [
"ansuman-satpathy:igvf13_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:35:24.648327+00:00",
"file_format": "tsv",
"file_size": 63259,
"href": "/tabular-files/IGVFFI1470AONX/@@download/IGVFFI1470AONX.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/e1b05952-0008-4cb4-864d-53364f513aea/IGVFFI1470AONX.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e13l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1833OZIZ/",
"accession": "IGVFDS1833OZIZ",
"aliases": [
"ansuman-satpathy:multiseq_igvf13_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1681DUIN/",
"accession": "IGVFDS1681DUIN",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf13_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3842BVTL/",
"accession": "IGVFDS3842BVTL",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf13_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": "2025-03-22T00:41:56.885091+00:00",
"sample_summary": "Homo sapiens multiplexed sample of left coronary artery",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM6422YWWA/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6422YWWA",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf13_10x1"
],
"classifications": [
"tissue",
"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/MONDO_0005010/",
"status": "released",
"term_name": "coronary artery disorder"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/1779b95c-3032-475b-8d7a-c607a2e42d32/",
"certificate_identifier": "IP115-09",
"controlled_access": true,
"data_use_limitation": "GRU",
"data_use_limitation_modifiers": [
"PUB"
],
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001626/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left coronary artery",
"term_name": "left coronary artery"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female, 48 years) left coronary artery tissue associated with coronary artery disorder; Homo sapiens (female, 73 years) left coronary artery tissue associated with coronary artery disorder; ... and 2 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": "2025-01-28T06:23:16.240916+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "b6beb82e-844e-4827-9200-bf3ae313b465",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}