{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS3556MYLH/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3556MYLH",
"aliases": [
"ansuman-satpathy:igvf17_analysis_set_10x5"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS3556MYLH](/analysis-sets/IGVFDS3556MYLH/) has `input_file_sets` with multiplexed samples: [IGVFSM8270UYGU](/multiplexed-samples/IGVFSM8270UYGU/) 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/IGVFDS3556MYLH/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS3556MYLH](/analysis-sets/IGVFDS3556MYLH/) 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/IGVFDS3556MYLH/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9430CLWM](/matrix-files/IGVFFI9430CLWM/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9430CLWM/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9430CLWM](/matrix-files/IGVFFI9430CLWM/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9430CLWM/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8270UYGU](/multiplexed-samples/IGVFSM8270UYGU/) 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/IGVFSM8270UYGU/"
}
]
},
"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": "2025-03-21T23:05:22.854965+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": "/index-files/IGVFFI4632DHVT/",
"accession": "IGVFFI4632DHVT",
"aliases": [
"ansuman-satpathy:igvf17_fragments_index_10x5"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:27.865446+00:00",
"file_format": "tbi",
"file_size": 1641314,
"href": "/index-files/IGVFFI4632DHVT/@@download/IGVFFI4632DHVT.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/d24a8890-77f9-47e3-863d-4c3da4df574f/IGVFFI4632DHVT.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l5_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1739UIIK/",
"accession": "IGVFFI1739UIIK",
"aliases": [
"ansuman-satpathy:igvf17_fragments_10x5"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:34:22.132552+00:00",
"file_format": "tsv",
"file_size": 4820799362,
"href": "/tabular-files/IGVFFI1739UIIK/@@download/IGVFFI1739UIIK.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/d1dea095-9d31-443d-a858-3bbee7fbe996/IGVFFI1739UIIK.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l5_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI0802WGXH/",
"accession": "IGVFFI0802WGXH",
"aliases": [
"ansuman-satpathy:igvf17_peaks_10x5"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:34:58.141149+00:00",
"file_format": "bed",
"file_size": 3080584,
"href": "/tabular-files/IGVFFI0802WGXH/@@download/IGVFFI0802WGXH.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/0f48ff99-c956-43ed-80a1-0cd9e2fc5761/IGVFFI0802WGXH.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l5_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI9430CLWM/",
"accession": "IGVFFI9430CLWM",
"aliases": [
"ansuman-satpathy:igvf17_raw_rna_counts_10x5"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:12:06.642671+00:00",
"file_format": "hdf5",
"file_size": 162778650,
"href": "/matrix-files/IGVFFI9430CLWM/@@download/IGVFFI9430CLWM.h5",
"s3_uri": "s3://igvf-files/2025/01/28/96e41ab1-7d9b-42f5-9e12-68b808a1e94b/IGVFFI9430CLWM.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l5_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7482FVKT/",
"accession": "IGVFFI7482FVKT",
"aliases": [
"ansuman-satpathy:igvf17_multiseq_count_matrix_10x5"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:36:51.322091+00:00",
"file_format": "tsv",
"file_size": 556675,
"href": "/tabular-files/IGVFFI7482FVKT/@@download/IGVFFI7482FVKT.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/5c4696cc-8b5a-45ca-a717-1fd2a091b8cb/IGVFFI7482FVKT.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e17l5_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9074YQHT/",
"accession": "IGVFDS9074YQHT",
"aliases": [
"ansuman-satpathy:multiseq_igvf17_10x5"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5600JMON/",
"accession": "IGVFDS5600JMON",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf17_10x5"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5452GNYG/",
"accession": "IGVFDS5452GNYG",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf17_10x5"
],
"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": "2025-03-22T00:45:03.544448+00:00",
"sample_summary": "Homo sapiens multiplexed sample of RUES2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8270UYGU/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8270UYGU",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf17_10x5"
],
"cellular_sub_pool": "5",
"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": "2025-01-28T06:34:22.132552+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "15eb9174-0d46-4531-85d1-6a265504faa6",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}