{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4694DHAU",
"aliases": [
"ansuman-satpathy:igvf13_analysis_set_10x4"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM4220ALCU](/multiplexed-samples/IGVFSM4220ALCU/) has in progress subobject tabular file [IGVFFI7218IPWP](/tabular-files/IGVFFI7218IPWP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM4220ALCU/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM4220ALCU](/multiplexed-samples/IGVFSM4220ALCU/) 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/IGVFSM4220ALCU/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4694DHAU](/analysis-sets/IGVFDS4694DHAU/) has `input_file_sets` with multiplexed samples: [IGVFSM4220ALCU](/multiplexed-samples/IGVFSM4220ALCU/) 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/IGVFDS4694DHAU/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4694DHAU](/analysis-sets/IGVFDS4694DHAU/) 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/IGVFDS4694DHAU/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7758BEID](/matrix-files/IGVFFI7758BEID/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7758BEID/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7758BEID](/matrix-files/IGVFFI7758BEID/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7758BEID/"
}
]
},
"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": "2025-03-21T23:05:07.265492+00:00",
"data_use_limitation_summaries": [
"GRU-PUB"
],
"donors": [
{
"@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"
},
{
"@id": "/human-donors/IGVFDO2120EMSK/",
"accession": "IGVFDO2120EMSK",
"aliases": [
"thomas-quertermous:LAD_multiome_donor1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI5245SKIU/",
"accession": "IGVFFI5245SKIU",
"aliases": [
"ansuman-satpathy:igvf13_fragments_10x4"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:26:23.978547+00:00",
"file_format": "tsv",
"file_size": 5518981036,
"href": "/tabular-files/IGVFFI5245SKIU/@@download/IGVFFI5245SKIU.tsv.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/7380c8b2-af18-41d9-a774-8897c0bc4a4e/IGVFFI5245SKIU.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l4_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI1499MFSV/",
"accession": "IGVFFI1499MFSV",
"aliases": [
"ansuman-satpathy:igvf13_fragments_index_10x4"
],
"content_type": "index",
"controlled_access": true,
"creation_timestamp": "2025-01-28T15:29:13.363615+00:00",
"file_format": "tbi",
"file_size": 1579515,
"href": "/index-files/IGVFFI1499MFSV/@@download/IGVFFI1499MFSV.tbi",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/715e82e5-8500-47d2-bbd0-8079e2ebec3e/IGVFFI1499MFSV.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l4_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1834ZPFR/",
"accession": "IGVFFI1834ZPFR",
"aliases": [
"ansuman-satpathy:igvf13_multiseq_count_matrix_10x4"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:35:48.361829+00:00",
"file_format": "tsv",
"file_size": 64707,
"href": "/tabular-files/IGVFFI1834ZPFR/@@download/IGVFFI1834ZPFR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/2ac179de-f28a-46b0-ad5e-c1be17d261fe/IGVFFI1834ZPFR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e13l4_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7945BILX/",
"accession": "IGVFFI7945BILX",
"aliases": [
"ansuman-satpathy:igvf13_peaks_10x4"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:27:00.802819+00:00",
"file_format": "bed",
"file_size": 715399,
"href": "/tabular-files/IGVFFI7945BILX/@@download/IGVFFI7945BILX.bed.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/1183ef39-cf4f-447f-beb8-6b64f82f2ed4/IGVFFI7945BILX.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l4_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI7758BEID/",
"accession": "IGVFFI7758BEID",
"aliases": [
"ansuman-satpathy:igvf13_raw_rna_counts_10x4"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:10:26.146746+00:00",
"file_format": "hdf5",
"file_size": 131004101,
"href": "/matrix-files/IGVFFI7758BEID/@@download/IGVFFI7758BEID.h5",
"s3_uri": "s3://igvf-files/2025/01/28/7790b675-f201-43cd-bba9-0ecab51374ed/IGVFFI7758BEID.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l4_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5059CAEA/",
"accession": "IGVFDS5059CAEA",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf13_10x4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS7173XOSJ/",
"accession": "IGVFDS7173XOSJ",
"aliases": [
"ansuman-satpathy:multiseq_igvf13_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2114XGWE/",
"accession": "IGVFDS2114XGWE",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf13_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": "2025-03-22T00:44:02.805898+00:00",
"sample_summary": "Homo sapiens multiplexed sample of left coronary artery",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4220ALCU/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM4220ALCU",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf13_10x4"
],
"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/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T06:26:23.978547+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "a807d08f-f5c7-44db-bbdf-e90b1496b5f3",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}