{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
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"aliases": [
"ansuman-satpathy:igvf9_analysis_set_10x2"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS6435ALNY](/analysis-sets/IGVFDS6435ALNY/) has `input_file_sets` with multiplexed samples: [IGVFSM2512OHNK](/multiplexed-samples/IGVFSM2512OHNK/) but no `demultiplexed_samples`. 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/IGVFDS6435ALNY/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS6435ALNY](/analysis-sets/IGVFDS6435ALNY/) 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/IGVFDS6435ALNY/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM2512OHNK](/multiplexed-samples/IGVFSM2512OHNK/) 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/IGVFSM2512OHNK/"
}
]
},
"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": "2025-03-21T23:04:42.717607+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/IGVFFI5180HSIX/",
"accession": "IGVFFI5180HSIX",
"aliases": [
"ansuman-satpathy:igvf9_peaks_10x2"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:03:06.084484+00:00",
"derived_from": [
"/tabular-files/IGVFFI4907GYFZ/"
],
"file_format": "bed",
"file_size": 1697553,
"href": "/tabular-files/IGVFFI5180HSIX/@@download/IGVFFI5180HSIX.bed.gz",
"md5sum": "5412f5fe0db774d833a05404accf13be",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/90f7efe5-1432-497f-afdd-cde6f09180ca/IGVFFI5180HSIX.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l2_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI7725ECTZ/",
"accession": "IGVFFI7725ECTZ",
"aliases": [
"ansuman-satpathy:igvf9_fragments_index_10x2"
],
"content_type": "index",
"controlled_access": true,
"creation_timestamp": "2025-01-28T15:28:22.638715+00:00",
"derived_from": [
"/tabular-files/IGVFFI4907GYFZ/"
],
"file_format": "tbi",
"file_size": 1737885,
"href": "/index-files/IGVFFI7725ECTZ/@@download/IGVFFI7725ECTZ.tbi",
"md5sum": "4c2b117dc0a7d880bfd21cb9553b09a4",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/bbf7bd78-3505-494c-8fcf-2e473fe3098b/IGVFFI7725ECTZ.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l2_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4907GYFZ/",
"accession": "IGVFFI4907GYFZ",
"aliases": [
"ansuman-satpathy:igvf9_fragments_10x2"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:02:33.757635+00:00",
"derived_from": [
"/sequence-files/IGVFFI9247KOVT/",
"/sequence-files/IGVFFI0270TTFC/",
"/sequence-files/IGVFFI4857JZLI/",
"/sequence-files/IGVFFI0126DWYC/",
"/sequence-files/IGVFFI0060PNZQ/",
"/sequence-files/IGVFFI4991KQMH/",
"/sequence-files/IGVFFI2875ZLRI/",
"/sequence-files/IGVFFI5847LLGI/",
"/sequence-files/IGVFFI8123QWYG/",
"/sequence-files/IGVFFI8454EASP/",
"/sequence-files/IGVFFI4156JJZJ/",
"/sequence-files/IGVFFI8332QYKO/"
],
"file_format": "tsv",
"file_size": 6639939248,
"href": "/tabular-files/IGVFFI4907GYFZ/@@download/IGVFFI4907GYFZ.tsv.gz",
"md5sum": "d82c0730a021ef69b13197aa04208a4a",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/6a7eef64-4e21-4b74-9cec-11ad77579632/IGVFFI4907GYFZ.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l2_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI5385WLKP/",
"accession": "IGVFFI5385WLKP",
"aliases": [
"ansuman-satpathy:igvf9_multiseq_count_matrix_10x2"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:32:03.865284+00:00",
"derived_from": [
"/sequence-files/IGVFFI9084LMNS/",
"/sequence-files/IGVFFI5210WSAO/",
"/sequence-files/IGVFFI2539LKSK/",
"/sequence-files/IGVFFI4990FLLB/",
"/sequence-files/IGVFFI8666ENEF/",
"/sequence-files/IGVFFI8268RJMJ/",
"/sequence-files/IGVFFI5623NAWQ/",
"/sequence-files/IGVFFI2295NKXK/",
"/sequence-files/IGVFFI9972WCVC/",
"/sequence-files/IGVFFI5429FBRE/",
"/sequence-files/IGVFFI0168UXWB/",
"/sequence-files/IGVFFI7210ATDK/"
],
"file_format": "tsv",
"file_size": 817022,
"href": "/tabular-files/IGVFFI5385WLKP/@@download/IGVFFI5385WLKP.tsv.gz",
"md5sum": "9a9f346a143b5c43007535b6a04f2633",
"s3_uri": "s3://igvf-files/2025/02/19/be87ae8c-fc48-46c6-a667-10a79f197227/IGVFFI5385WLKP.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e9l2_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI2733DASR/",
"accession": "IGVFFI2733DASR",
"aliases": [
"ansuman-satpathy:igvf9_raw_rna_counts_10x2"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:37:54.482234+00:00",
"derived_from": [
"/sequence-files/IGVFFI3919MNJT/",
"/sequence-files/IGVFFI9202YRAH/",
"/sequence-files/IGVFFI3552KANN/",
"/sequence-files/IGVFFI8045BKNA/",
"/sequence-files/IGVFFI2674MLDJ/",
"/sequence-files/IGVFFI4573DBVN/",
"/sequence-files/IGVFFI5886WMKB/",
"/sequence-files/IGVFFI4871CJVP/",
"/sequence-files/IGVFFI9011EHAQ/",
"/sequence-files/IGVFFI0366NSOV/",
"/sequence-files/IGVFFI5584TCVB/",
"/sequence-files/IGVFFI9988VCOT/"
],
"file_format": "hdf5",
"file_size": 218377467,
"href": "/matrix-files/IGVFFI2733DASR/@@download/IGVFFI2733DASR.h5",
"md5sum": "1c263f35ae013777352ff154fb15626a",
"s3_uri": "s3://igvf-files/2025/01/28/d018b13c-2c2b-4af6-be99-0e9fa38f9fb0/IGVFFI2733DASR.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf9/e9l2_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3446FAJU/",
"accession": "IGVFDS3446FAJU",
"aliases": [
"ansuman-satpathy:multiseq_igvf9_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4370KUWU/",
"accession": "IGVFDS4370KUWU",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf9_10x2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2108XESQ/",
"accession": "IGVFDS2108XESQ",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf9_10x2"
],
"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": "2025-03-22T00:42:51.247704+00:00",
"sample_summary": "Homo sapiens multiplexed sample of B cell",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2512OHNK/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2512OHNK",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf9_10x2"
],
"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": "10",
"status": "released",
"submitted_by": {
"@id": "/users/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T06:02:33.757635+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "cc73d4fe-addf-482e-8464-a7d168df695a",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}