{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS3457PPSX/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3457PPSX",
"aliases": [
"ansuman-satpathy:igvf17_analysis_set_10x3"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7718TGMZ](/matrix-files/IGVFFI7718TGMZ/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7718TGMZ/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7718TGMZ](/matrix-files/IGVFFI7718TGMZ/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7718TGMZ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM6345RLEH](/multiplexed-samples/IGVFSM6345RLEH/) 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/IGVFSM6345RLEH/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS3457PPSX](/analysis-sets/IGVFDS3457PPSX/) has `input_file_sets` with multiplexed samples: [IGVFSM6345RLEH](/multiplexed-samples/IGVFSM6345RLEH/) 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/IGVFDS3457PPSX/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS3457PPSX](/analysis-sets/IGVFDS3457PPSX/) 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/IGVFDS3457PPSX/"
}
]
},
"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": "2025-03-21T23:05:19.987749+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO5261UCLF/",
"accession": "IGVFDO5261UCLF",
"aliases": [
"igvf:donor_of_RUES2",
"igvf:donor_RUES2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI9112WEDK/",
"accession": "IGVFFI9112WEDK",
"aliases": [
"ansuman-satpathy:igvf17_peaks_10x3"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:32:45.775086+00:00",
"file_format": "bed",
"file_size": 3182619,
"href": "/tabular-files/IGVFFI9112WEDK/@@download/IGVFFI9112WEDK.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/c6ee4504-97a9-48cf-bd5d-c2882b756e34/IGVFFI9112WEDK.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l3_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI8360SRWO/",
"accession": "IGVFFI8360SRWO",
"aliases": [
"ansuman-satpathy:igvf17_fragments_10x3"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:32:05.828644+00:00",
"file_format": "tsv",
"file_size": 5101000778,
"href": "/tabular-files/IGVFFI8360SRWO/@@download/IGVFFI8360SRWO.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/a7c9c3df-e5cf-4518-ac6f-8778c0c2b68c/IGVFFI8360SRWO.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l3_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI7718TGMZ/",
"accession": "IGVFFI7718TGMZ",
"aliases": [
"ansuman-satpathy:igvf17_raw_rna_counts_10x3"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:11:36.924207+00:00",
"file_format": "hdf5",
"file_size": 165028915,
"href": "/matrix-files/IGVFFI7718TGMZ/@@download/IGVFFI7718TGMZ.h5",
"s3_uri": "s3://igvf-files/2025/01/28/01c0b63e-7e79-4863-853f-52d24bd63e5c/IGVFFI7718TGMZ.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l3_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI0707ZMKE/",
"accession": "IGVFFI0707ZMKE",
"aliases": [
"ansuman-satpathy:igvf17_multiseq_count_matrix_10x3"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:36:31.259372+00:00",
"file_format": "tsv",
"file_size": 621815,
"href": "/tabular-files/IGVFFI0707ZMKE/@@download/IGVFFI0707ZMKE.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/285d0cac-2db9-4c1c-b135-db33109a187b/IGVFFI0707ZMKE.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e17l3_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI3180EJTY/",
"accession": "IGVFFI3180EJTY",
"aliases": [
"ansuman-satpathy:igvf17_fragments_index_10x3"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:23.612215+00:00",
"file_format": "tbi",
"file_size": 1689752,
"href": "/index-files/IGVFFI3180EJTY/@@download/IGVFFI3180EJTY.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/2b366fc3-72d4-4b41-8ce1-19ba451523b2/IGVFFI3180EJTY.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l3_fragments.tsv.gz.tbi",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7632NJZU/",
"accession": "IGVFDS7632NJZU",
"aliases": [
"ansuman-satpathy:multiseq_igvf17_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2170OFES/",
"accession": "IGVFDS2170OFES",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf17_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1850HDEG/",
"accession": "IGVFDS1850HDEG",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf17_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": "2025-03-22T00:44:51.116734+00:00",
"sample_summary": "Homo sapiens multiplexed sample of RUES2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM6345RLEH/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6345RLEH",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf17_10x3"
],
"cellular_sub_pool": "3",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/49ea766d-c6ef-4ced-be8c-4e3ba1693d31/",
"certificate_identifier": "IP115-24",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "RUES2",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 2 days; Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 1 day; ... 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": "2025-01-28T06:32:05.828644+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "c7c4a207-8111-403d-bfb3-77f389c59cd6",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}