{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS9664YLAD/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9664YLAD",
"aliases": [
"ansuman-satpathy:igvf10_analysis_set_10x2"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM0539NUPM](/multiplexed-samples/IGVFSM0539NUPM/) 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/IGVFSM0539NUPM/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS9664YLAD](/analysis-sets/IGVFDS9664YLAD/) has `input_file_sets` with multiplexed samples: [IGVFSM0539NUPM](/multiplexed-samples/IGVFSM0539NUPM/) 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/IGVFDS9664YLAD/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS9664YLAD](/analysis-sets/IGVFDS9664YLAD/) 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/IGVFDS9664YLAD/"
},
{
"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": "mismatched status",
"detail": "Released matrix file [IGVFFI5029LHBH](/matrix-files/IGVFFI5029LHBH/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI5029LHBH/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI5029LHBH](/matrix-files/IGVFFI5029LHBH/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI5029LHBH/"
}
]
},
"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": "2025-03-21T23:04:44.733540+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"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/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"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": "/index-files/IGVFFI6088AFLH/",
"accession": "IGVFFI6088AFLH",
"aliases": [
"ansuman-satpathy:igvf10_fragments_index_10x2"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:27.159098+00:00",
"file_format": "tbi",
"file_size": 2191109,
"href": "/index-files/IGVFFI6088AFLH/@@download/IGVFFI6088AFLH.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/bafec659-39d9-44a8-91aa-4e60f0dd0f7e/IGVFFI6088AFLH.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l2_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7411STSC/",
"accession": "IGVFFI7411STSC",
"aliases": [
"ansuman-satpathy:igvf10_peaks_10x2"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:06:13.955869+00:00",
"file_format": "bed",
"file_size": 1570325,
"href": "/tabular-files/IGVFFI7411STSC/@@download/IGVFFI7411STSC.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/79774340-e7e6-45b9-851f-6104376fb0fd/IGVFFI7411STSC.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l2_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI9254IQXZ/",
"accession": "IGVFFI9254IQXZ",
"aliases": [
"ansuman-satpathy:igvf10_fragments_10x2"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:05:29.138870+00:00",
"file_format": "tsv",
"file_size": 8833663458,
"href": "/tabular-files/IGVFFI9254IQXZ/@@download/IGVFFI9254IQXZ.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/331ffd7e-4f54-48c9-b377-ede5479f12bf/IGVFFI9254IQXZ.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l2_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI4526HCTX/",
"accession": "IGVFFI4526HCTX",
"aliases": [
"ansuman-satpathy:igvf10_multiseq_count_matrix_10x2"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:32:23.651657+00:00",
"file_format": "tsv",
"file_size": 883404,
"href": "/tabular-files/IGVFFI4526HCTX/@@download/IGVFFI4526HCTX.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/79a88d4e-bd52-4acb-af5c-3c8ca61fc55d/IGVFFI4526HCTX.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e10l2_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI5029LHBH/",
"accession": "IGVFFI5029LHBH",
"aliases": [
"ansuman-satpathy:igvf10_raw_rna_counts_10x2"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:38:37.894286+00:00",
"file_format": "hdf5",
"file_size": 275110797,
"href": "/matrix-files/IGVFFI5029LHBH/@@download/IGVFFI5029LHBH.h5",
"s3_uri": "s3://igvf-files/2025/01/28/992a9700-fa74-470d-baef-2a3c719ef502/IGVFFI5029LHBH.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l2_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6521MNHG/",
"accession": "IGVFDS6521MNHG",
"aliases": [
"ansuman-satpathy:multiseq_igvf10_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9139TBCB/",
"accession": "IGVFDS9139TBCB",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf10_10x2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1013HCXI/",
"accession": "IGVFDS1013HCXI",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf10_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": "2025-03-22T00:42:57.224616+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/IGVFSM0539NUPM/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM0539NUPM",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf10_10x2"
],
"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_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_type": "protein"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T06:05:29.138870+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "2e68ed39-4594-47a6-8fbb-3613164d6f31",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}