{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5448FWBW",
"aliases": [
"ansuman-satpathy:igvf0_analysis_set"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI3143UHIU](/matrix-files/IGVFFI3143UHIU/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI3143UHIU/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI3143UHIU](/matrix-files/IGVFFI3143UHIU/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI3143UHIU/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS5448FWBW](/analysis-sets/IGVFDS5448FWBW/) has `input_file_sets` with multiplexed samples: [IGVFSM2682GVVD](/multiplexed-samples/IGVFSM2682GVVD/) 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/IGVFDS5448FWBW/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2025-01-28T05:35:01.189264+00:00",
"description": "Quality-control workflow performed by Satpathy Lab - WTC11 endothelial differentiation",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI9532SPYG/",
"accession": "IGVFFI9532SPYG",
"aliases": [
"ansuman-satpathy:igvf0_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-02-14T22:58:12.890513+00:00",
"file_format": "tsv",
"file_size": 5940246010,
"href": "/tabular-files/IGVFFI9532SPYG/@@download/IGVFFI9532SPYG.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/14/68cec871-30ef-45c7-bd63-034f7de3b521/IGVFFI9532SPYG.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI0480XBYK/",
"accession": "IGVFFI0480XBYK",
"aliases": [
"ansuman-satpathy:igvf0_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-02-14T22:58:39.317295+00:00",
"file_format": "bed",
"file_size": 2482339,
"href": "/tabular-files/IGVFFI0480XBYK/@@download/IGVFFI0480XBYK.bed.gz",
"s3_uri": "s3://igvf-files/2025/02/14/41079c9c-2a35-4ca4-9e45-edde57b43857/IGVFFI0480XBYK.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_peaks.bed.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI7419FNVX/",
"accession": "IGVFFI7419FNVX",
"aliases": [
"ansuman-satpathy:igvf0_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-02-14T23:07:50.477488+00:00",
"file_format": "tbi",
"file_size": 1841747,
"href": "/index-files/IGVFFI7419FNVX/@@download/IGVFFI7419FNVX.tbi",
"s3_uri": "s3://igvf-files/2025/02/14/e41186fe-2bbc-43f2-b46e-2765086fbe86/IGVFFI7419FNVX.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI3143UHIU/",
"accession": "IGVFFI3143UHIU",
"aliases": [
"ansuman-satpathy:igvf0_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-02-14T23:18:31.500791+00:00",
"file_format": "hdf5",
"file_size": 167840704,
"href": "/matrix-files/IGVFFI3143UHIU/@@download/IGVFFI3143UHIU.h5",
"s3_uri": "s3://igvf-files/2025/02/14/32bb4e55-31e5-4b93-8c7d-79b89da4af25/IGVFFI3143UHIU.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI0978MWOP/",
"accession": "IGVFFI0978MWOP",
"aliases": [
"ansuman-satpathy:igvf0_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:37:22.781642+00:00",
"file_format": "tsv",
"file_size": 402543,
"href": "/tabular-files/IGVFFI0978MWOP/@@download/IGVFFI0978MWOP.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/c5a606ff-6a7f-4a54-a1cf-22b8a4d60523/IGVFFI0978MWOP.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e0l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS7482RDGX/",
"accession": "IGVFDS7482RDGX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf0_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6243XJYN/",
"accession": "IGVFDS6243XJYN",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf0_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS4882ESVG/",
"accession": "IGVFDS4882ESVG",
"aliases": [
"ansuman-satpathy:multiseq_igvf0_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"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": "2025-03-07T06:03:59.380337+00:00",
"sample_summary": "GM25256 (WTC-11) differentiated cell specimen and multiplexed sample",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2682GVVD/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2682GVVD",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf0_10x1"
],
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: GM25256 (WTC-11) differentiated cell specimen induced to endothelial cell for 3 days, male, Homo sapiens; GM25256 (WTC-11) differentiated cell specimen induced to endothelial cell for 4 days, male, Homo sapiens; ... and 21 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": "2025-02-14T22:58:12.890513+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "c78d6894-d521-4532-ba34-364310e8a357",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}