{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0793KZKS",
"aliases": [
"ansuman-satpathy:igvf12_analysis_set",
"ansuman-satpathy:igvf12_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM3641EGVH](/multiplexed-samples/IGVFSM3641EGVH/) has in progress subobject tabular file [IGVFFI6870GMPP](/tabular-files/IGVFFI6870GMPP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM3641EGVH/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7332UUZE](/matrix-files/IGVFFI7332UUZE/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7332UUZE/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7332UUZE](/matrix-files/IGVFFI7332UUZE/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7332UUZE/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS0793KZKS](/analysis-sets/IGVFDS0793KZKS/) has `input_file_sets` with multiplexed samples: [IGVFSM3641EGVH](/multiplexed-samples/IGVFSM3641EGVH/) 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/IGVFDS0793KZKS/"
}
]
},
"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": "2025-01-28T05:34:49.231150+00:00",
"data_use_limitation_summaries": [
"GRU"
],
"description": "Quality-control workflow performed by Satpathy Lab - Primary B cell differentiation, human bone marrow",
"donors": [
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"aliases": [
"ansuman-satpathy:singh_bcell_donor_2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1264SGCS/",
"accession": "IGVFDO1264SGCS",
"aliases": [
"ansuman-satpathy:bridge_bone_marrow_donor_2038"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI1928OJPU/",
"accession": "IGVFFI1928OJPU",
"aliases": [
"ansuman-satpathy:igvf12_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:10:42.454640+00:00",
"file_format": "bed",
"file_size": 1211084,
"href": "/tabular-files/IGVFFI1928OJPU/@@download/IGVFFI1928OJPU.bed.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/03f0b3cb-9b12-4c73-b97d-e213da3a1a57/IGVFFI1928OJPU.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI7212WXZR/",
"accession": "IGVFFI7212WXZR",
"aliases": [
"ansuman-satpathy:igvf12_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:09:51.104664+00:00",
"file_format": "tsv",
"file_size": 4301303865,
"href": "/tabular-files/IGVFFI7212WXZR/@@download/IGVFFI7212WXZR.tsv.gz",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/d3ab9d9e-b066-4380-93c1-485badc91725/IGVFFI7212WXZR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI9775WVZK/",
"accession": "IGVFFI9775WVZK",
"aliases": [
"ansuman-satpathy:igvf12_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": true,
"creation_timestamp": "2025-01-28T15:28:36.161759+00:00",
"file_format": "tbi",
"file_size": 1581923,
"href": "/index-files/IGVFFI9775WVZK/@@download/IGVFFI9775WVZK.tbi",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/d08cad8d-e217-4316-8b61-8fb8301de69e/IGVFFI9775WVZK.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI7332UUZE/",
"accession": "IGVFFI7332UUZE",
"aliases": [
"ansuman-satpathy:igvf12_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:06:55.795503+00:00",
"file_format": "hdf5",
"file_size": 158105339,
"href": "/matrix-files/IGVFFI7332UUZE/@@download/IGVFFI7332UUZE.h5",
"s3_uri": "s3://igvf-files/2025/01/28/42c21b7d-ada7-46ff-9859-73b9306d38f0/IGVFFI7332UUZE.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1257TMRU/",
"accession": "IGVFFI1257TMRU",
"aliases": [
"ansuman-satpathy:igvf12_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:33:01.941468+00:00",
"file_format": "tsv",
"file_size": 183094,
"href": "/tabular-files/IGVFFI1257TMRU/@@download/IGVFFI1257TMRU.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/86ac9cbc-42f6-401d-94b9-ae1aee86000e/IGVFFI1257TMRU.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e12l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1570UJMU/",
"accession": "IGVFDS1570UJMU",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf12_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS7563XAXA/",
"accession": "IGVFDS7563XAXA",
"aliases": [
"ansuman-satpathy:multiseq_igvf12_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8103FALC/",
"accession": "IGVFDS8103FALC",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf12_10x1"
],
"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": "2025-03-22T00:41:49.219995+00:00",
"sample_summary": "multiplexed sample of B cell, bone marrow",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM3641EGVH/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM3641EGVH",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf12_10x1"
],
"classifications": [
"differentiated cell specimen",
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/1e03eda3-a983-4cee-864e-43acb4c1b186/",
"certificate_identifier": "IP115-18",
"controlled_access": true,
"data_use_limitation": "GRU",
"status": "released"
},
{
"@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"
},
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T06:09:51.104664+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "df27a336-c1f4-4f5e-9aab-1c9952e91851",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}