{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4963SRAJ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4963SRAJ",
"aliases": [
"ansuman-satpathy:igvf18_analysis_set",
"ansuman-satpathy:igvf18_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4963SRAJ](/analysis-sets/IGVFDS4963SRAJ/) has `input_file_sets` with multiplexed samples: [IGVFSM4392KEFB](/multiplexed-samples/IGVFSM4392KEFB/) 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/IGVFDS4963SRAJ/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4963SRAJ](/analysis-sets/IGVFDS4963SRAJ/) 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/IGVFDS4963SRAJ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM4392KEFB](/multiplexed-samples/IGVFSM4392KEFB/) 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/IGVFSM4392KEFB/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
}
]
},
"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": "2025-01-28T05:34:59.931160+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - IMR90, MCF7, HCT116, SK-N-SH, HUDEP2 erythroid differentiation, teloHAEC +/- yoda1",
"donors": [
{
"@id": "/human-donors/IGVFDO4200NZSV/",
"accession": "IGVFDO4200NZSV",
"aliases": [
"igvf:donor_of_IMR90"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7503RZHO/",
"accession": "IGVFDO7503RZHO",
"aliases": [
"igvf:donor_of_MCF7"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0965QSBA/",
"accession": "IGVFDO0965QSBA",
"aliases": [
"igvf:donor_of_HUDEP-2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9018OPIO/",
"accession": "IGVFDO9018OPIO",
"aliases": [
"igvf:donor_of_SKNSH"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI6686KVZP/",
"accession": "IGVFFI6686KVZP",
"aliases": [
"ansuman-satpathy:igvf18_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:35:27.353847+00:00",
"derived_from": [
"/sequence-files/IGVFFI7773BPEF/",
"/sequence-files/IGVFFI2427ACWP/",
"/sequence-files/IGVFFI2590TULH/",
"/sequence-files/IGVFFI4076GAUO/"
],
"file_format": "tsv",
"file_size": 4861826661,
"href": "/tabular-files/IGVFFI6686KVZP/@@download/IGVFFI6686KVZP.tsv.gz",
"md5sum": "ecc96fa422cbb7d8edf5ad1ae8941b8d",
"s3_uri": "s3://igvf-files/2025/01/28/2175e14e-9c46-4bd7-ae69-5e24b6e852c0/IGVFFI6686KVZP.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf18/e18l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI0022NNBQ/",
"accession": "IGVFFI0022NNBQ",
"aliases": [
"ansuman-satpathy:igvf18_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:35:54.972031+00:00",
"derived_from": [
"/tabular-files/IGVFFI6686KVZP/"
],
"file_format": "bed",
"file_size": 1648060,
"href": "/tabular-files/IGVFFI0022NNBQ/@@download/IGVFFI0022NNBQ.bed.gz",
"md5sum": "0e371977efc17bfaa7294fe0eef1b655",
"s3_uri": "s3://igvf-files/2025/01/28/7633400b-f9a6-4473-8976-79bf2285da80/IGVFFI0022NNBQ.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf18/e18l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI1435XKIF/",
"accession": "IGVFFI1435XKIF",
"aliases": [
"ansuman-satpathy:igvf18_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:30.162528+00:00",
"derived_from": [
"/tabular-files/IGVFFI6686KVZP/"
],
"file_format": "tbi",
"file_size": 1646363,
"href": "/index-files/IGVFFI1435XKIF/@@download/IGVFFI1435XKIF.tbi",
"md5sum": "82f20f80e1b75468f0abfcd141cd5539",
"s3_uri": "s3://igvf-files/2025/01/28/767e4b27-7c54-41f9-b35d-4035ded68eb7/IGVFFI1435XKIF.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf18/e18l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI9541YCAE/",
"accession": "IGVFFI9541YCAE",
"aliases": [
"ansuman-satpathy:igvf18_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:12:20.229354+00:00",
"derived_from": [
"/sequence-files/IGVFFI5616SZRW/",
"/sequence-files/IGVFFI1988QWCI/",
"/sequence-files/IGVFFI6526OBMG/",
"/sequence-files/IGVFFI8737QQSV/"
],
"file_format": "hdf5",
"file_size": 184876769,
"href": "/matrix-files/IGVFFI9541YCAE/@@download/IGVFFI9541YCAE.h5",
"md5sum": "6e64d970abf48bb0888366e2b0d6f98d",
"s3_uri": "s3://igvf-files/2025/01/28/b1110860-fa6f-44a1-a1c8-1b7dfdd3b314/IGVFFI9541YCAE.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf18/e18l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9158ZCDS/",
"accession": "IGVFFI9158ZCDS",
"aliases": [
"ansuman-satpathy:igvf18_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:37:00.634789+00:00",
"derived_from": [
"/sequence-files/IGVFFI2894YADS/",
"/sequence-files/IGVFFI1882TZQH/",
"/sequence-files/IGVFFI9425XUHZ/"
],
"file_format": "tsv",
"file_size": 747058,
"href": "/tabular-files/IGVFFI9158ZCDS/@@download/IGVFFI9158ZCDS.tsv.gz",
"md5sum": "7a8b23ad1092a4e9d91dce5b299755c7",
"s3_uri": "s3://igvf-files/2025/02/19/a528b79a-cd1e-4e38-9371-fc14b20cf746/IGVFFI9158ZCDS.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e18l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1427CODJ/",
"accession": "IGVFDS1427CODJ",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf18_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS7168GITK/",
"accession": "IGVFDS7168GITK",
"aliases": [
"ansuman-satpathy:multiseq_igvf18_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1210CYWP/",
"accession": "IGVFDS1210CYWP",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf18_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": "2025-03-07T06:05:33.255947+00:00",
"sample_summary": "Homo sapiens multiplexed sample of HCT116, HUDEP-2, IMR-90, MCF-7, SK-N-SH, TeloHAEC, perturbed with 3 μM Yoda1 for 4 hours",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4392KEFB/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM4392KEFB",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf18_10x1"
],
"cellular_sub_pool": "1",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/20743336-7ae0-4e51-ab85-4ef4401b9b7d/",
"certificate_identifier": "IP115-16",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/4ff60cda-a674-443c-8864-009fa16b9f43/",
"certificate_identifier": "IP115-25",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001196/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "IMR-90",
"term_name": "IMR-90"
},
{
"@id": "/sample-terms/EFO_0001203/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "MCF-7",
"term_name": "MCF-7"
},
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
},
{
"@id": "/sample-terms/EFO_0003072/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:SK-N-SH"
],
"status": "released",
"summary": "SK-N-SH",
"term_name": "SK-N-SH"
},
{
"@id": "/sample-terms/EFO_0022838/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HUDEP-2"
],
"status": "released",
"summary": "HUDEP-2",
"term_name": "HUDEP-2"
},
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) IMR-90 cell line; Homo sapiens (female) MCF-7 cell line; ... and 17 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 3 μM Yoda1 for 4 hours",
"treatment_term_name": "Yoda1",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T06:35:27.353847+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "5a658940-a8fa-4c98-9fb0-3bb6063c0815",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}