{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS2269RNLP/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2269RNLP",
"aliases": [
"ansuman-satpathy:igvf9_analysis_set_10x3"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS2269RNLP](/analysis-sets/IGVFDS2269RNLP/) has `input_file_sets` with multiplexed samples: [IGVFSM2794HHHZ](/multiplexed-samples/IGVFSM2794HHHZ/) 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/IGVFDS2269RNLP/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS2269RNLP](/analysis-sets/IGVFDS2269RNLP/) 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/IGVFDS2269RNLP/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9287XJLK](/matrix-files/IGVFFI9287XJLK/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9287XJLK/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9287XJLK](/matrix-files/IGVFFI9287XJLK/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9287XJLK/"
},
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM2794HHHZ](/multiplexed-samples/IGVFSM2794HHHZ/) has in progress subobject tabular file [IGVFFI8866FURX](/tabular-files/IGVFFI8866FURX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM2794HHHZ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM2794HHHZ](/multiplexed-samples/IGVFSM2794HHHZ/) 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/IGVFSM2794HHHZ/"
}
]
},
"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": "2025-03-21T23:04:43.727741+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI2552BEQA/",
"accession": "IGVFFI2552BEQA",
"aliases": [
"ansuman-satpathy:igvf9_peaks_10x3"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:04:00.683622+00:00",
"file_format": "bed",
"file_size": 1609396,
"href": "/tabular-files/IGVFFI2552BEQA/@@download/IGVFFI2552BEQA.bed.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/40cba417-e869-4ad4-81b2-b1c4e36fc965/IGVFFI2552BEQA.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l3_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI0965SWBT/",
"accession": "IGVFFI0965SWBT",
"aliases": [
"ansuman-satpathy:igvf9_fragments_10x3"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:03:27.580332+00:00",
"file_format": "tsv",
"file_size": 6613857519,
"href": "/tabular-files/IGVFFI0965SWBT/@@download/IGVFFI0965SWBT.tsv.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/ed432411-fb5d-4430-a354-cdf67662a3a2/IGVFFI0965SWBT.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l3_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI0598WSIG/",
"accession": "IGVFFI0598WSIG",
"aliases": [
"ansuman-satpathy:igvf9_fragments_index_10x3"
],
"content_type": "index",
"controlled_access": true,
"creation_timestamp": "2025-01-28T15:28:24.192276+00:00",
"file_format": "tbi",
"file_size": 1725026,
"href": "/index-files/IGVFFI0598WSIG/@@download/IGVFFI0598WSIG.tbi",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/c52003c7-76ee-47a5-9530-a5c25f400960/IGVFFI0598WSIG.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l3_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1424EJJW/",
"accession": "IGVFFI1424EJJW",
"aliases": [
"ansuman-satpathy:igvf9_multiseq_count_matrix_10x3"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:32:10.372753+00:00",
"file_format": "tsv",
"file_size": 838249,
"href": "/tabular-files/IGVFFI1424EJJW/@@download/IGVFFI1424EJJW.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/d2a116a0-440f-4093-b138-d7e701b7fbe8/IGVFFI1424EJJW.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e9l3_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI9287XJLK/",
"accession": "IGVFFI9287XJLK",
"aliases": [
"ansuman-satpathy:igvf9_raw_rna_counts_10x3"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:38:08.770663+00:00",
"file_format": "hdf5",
"file_size": 280230932,
"href": "/matrix-files/IGVFFI9287XJLK/@@download/IGVFFI9287XJLK.h5",
"s3_uri": "s3://igvf-files/2025/01/28/39c79548-7169-4c92-9c82-1374cb0ea830/IGVFFI9287XJLK.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l3_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4415ANKP/",
"accession": "IGVFDS4415ANKP",
"aliases": [
"ansuman-satpathy:multiseq_igvf9_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1742BLLN/",
"accession": "IGVFDS1742BLLN",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf9_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9385ZIKY/",
"accession": "IGVFDS9385ZIKY",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf9_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": "2025-03-22T00:42:53.933588+00:00",
"sample_summary": "Homo sapiens multiplexed sample of B cell",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2794HHHZ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2794HHHZ",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf9_10x3"
],
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/460c2060-3b32-43c1-ab4b-b2ef0fbeb2b2/",
"certificate_identifier": "IP115-22",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "B cell",
"term_name": "B cell"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 1 day; Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 5 days; ... and 5 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": "2025-01-28T06:03:27.580332+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "c780ffed-f2e5-462d-b527-44a3041ca6af",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}