{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2018URDY",
"aliases": [
"ansuman-satpathy:igvf10_analysis_set",
"ansuman-satpathy:igvf10_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS2018URDY](/analysis-sets/IGVFDS2018URDY/) has `input_file_sets` with multiplexed samples: [IGVFSM4547BFMA](/multiplexed-samples/IGVFSM4547BFMA/) 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/IGVFDS2018URDY/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS2018URDY](/analysis-sets/IGVFDS2018URDY/) 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/IGVFDS2018URDY/"
},
{
"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/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM4547BFMA](/multiplexed-samples/IGVFSM4547BFMA/) 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/IGVFSM4547BFMA/"
}
]
},
"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": "2025-01-28T05:34:45.163385+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - K562-CRISPRi, THP1, Jurkat, Jurkat + CD3/PMA, TeloHAEC-CRISPRi",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"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"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI0627MDWY/",
"accession": "IGVFFI0627MDWY",
"aliases": [
"ansuman-satpathy:igvf10_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:04:23.579216+00:00",
"derived_from": [
"/sequence-files/IGVFFI1562OZKE/",
"/sequence-files/IGVFFI6421BIVI/",
"/sequence-files/IGVFFI5662ZYXD/",
"/sequence-files/IGVFFI4218WPJB/",
"/sequence-files/IGVFFI9550CRCV/",
"/sequence-files/IGVFFI0859TDIG/",
"/sequence-files/IGVFFI8243RHWY/",
"/sequence-files/IGVFFI5047YIPF/"
],
"file_format": "tsv",
"file_size": 7834091145,
"href": "/tabular-files/IGVFFI0627MDWY/@@download/IGVFFI0627MDWY.tsv.gz",
"md5sum": "c69fb4ea81ca5efb0834a597ffe6e12c",
"s3_uri": "s3://igvf-files/2025/01/28/c9327329-e14b-4d32-a5ca-d5244c913121/IGVFFI0627MDWY.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI8318PQLH/",
"accession": "IGVFFI8318PQLH",
"aliases": [
"ansuman-satpathy:igvf10_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:04:59.601686+00:00",
"derived_from": [
"/tabular-files/IGVFFI0627MDWY/"
],
"file_format": "bed",
"file_size": 1579178,
"href": "/tabular-files/IGVFFI8318PQLH/@@download/IGVFFI8318PQLH.bed.gz",
"md5sum": "2979cc6717aa4bae4098efa856b23ea8",
"s3_uri": "s3://igvf-files/2025/01/28/d0d796bb-9bd7-4712-a2b8-ae957fb74b44/IGVFFI8318PQLH.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI3930OIYP/",
"accession": "IGVFFI3930OIYP",
"aliases": [
"ansuman-satpathy:igvf10_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:25.621373+00:00",
"derived_from": [
"/tabular-files/IGVFFI0627MDWY/"
],
"file_format": "tbi",
"file_size": 2058985,
"href": "/index-files/IGVFFI3930OIYP/@@download/IGVFFI3930OIYP.tbi",
"md5sum": "abb247b297226d16f586a20ae0771d0a",
"s3_uri": "s3://igvf-files/2025/01/28/e6d13c95-61c9-4a34-8337-316112635273/IGVFFI3930OIYP.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI2641LMFU/",
"accession": "IGVFFI2641LMFU",
"aliases": [
"ansuman-satpathy:igvf10_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:38:23.051464+00:00",
"derived_from": [
"/sequence-files/IGVFFI1373PDRD/",
"/sequence-files/IGVFFI7974OSGQ/",
"/sequence-files/IGVFFI6458EKNW/",
"/sequence-files/IGVFFI9291IGJI/",
"/sequence-files/IGVFFI5532UPHV/",
"/sequence-files/IGVFFI6544ROSI/",
"/sequence-files/IGVFFI5700XSJN/",
"/sequence-files/IGVFFI2521NNNE/"
],
"file_format": "hdf5",
"file_size": 250701921,
"href": "/matrix-files/IGVFFI2641LMFU/@@download/IGVFFI2641LMFU.h5",
"md5sum": "ee77c8bc88b1ebbf2fd2c076f5f04ebf",
"s3_uri": "s3://igvf-files/2025/01/28/72d9e9b2-440f-447e-8922-c19245eebb4e/IGVFFI2641LMFU.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5156ENLL/",
"accession": "IGVFFI5156ENLL",
"aliases": [
"ansuman-satpathy:igvf10_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:32:16.726610+00:00",
"derived_from": [
"/sequence-files/IGVFFI9013NTHD/",
"/sequence-files/IGVFFI9573QFAM/",
"/sequence-files/IGVFFI0918KPYX/",
"/sequence-files/IGVFFI6869BZEB/",
"/sequence-files/IGVFFI4769MROL/",
"/sequence-files/IGVFFI1030BVRK/",
"/sequence-files/IGVFFI8481VUXS/",
"/sequence-files/IGVFFI8633CYXB/"
],
"file_format": "tsv",
"file_size": 719645,
"href": "/tabular-files/IGVFFI5156ENLL/@@download/IGVFFI5156ENLL.tsv.gz",
"md5sum": "e4303887dd5881a7d68c2e99f9b373a6",
"s3_uri": "s3://igvf-files/2025/02/19/8ae35e9c-9006-4252-b2d7-e7ba29aa1a32/IGVFFI5156ENLL.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e10l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS3910GBDQ/",
"accession": "IGVFDS3910GBDQ",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf10_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS9295POCI/",
"accession": "IGVFDS9295POCI",
"aliases": [
"ansuman-satpathy:multiseq_igvf10_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2246RAZO/",
"accession": "IGVFDS2246RAZO",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf10_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": "2025-03-07T06:04:55.006806+00:00",
"sample_summary": "Homo sapiens multiplexed sample of Jurkat, K562, THP-1, TeloHAEC, stimulated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPRi Sp-dCas9-KOX1-KRAB",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4547BFMA/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM4547BFMA",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf10_10x1"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/4ff60cda-a674-443c-8864-009fa16b9f43/",
"certificate_identifier": "IP115-25",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
},
{
"@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 (male) Jurkat cell line treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; Homo sapiens (female) K562 cell line modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_term_name": "phorbol 13-acetate 12-myristate",
"treatment_type": "chemical"
},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain",
"treatment_type": "protein"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T06:04:23.579216+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "4db965e6-265f-4a06-8c97-206cfaf32de9",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}