{
"@context": "/terms/",
"@id": "/multiplexed-samples/IGVFSM0539NUPM/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM0539NUPM",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf10_10x2"
],
"audit": {
"INTERNAL_ACTION": [
{
"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"
},
"barcode_map": "/tabular-files/IGVFFI1855MTKY/",
"biomarkers": [],
"classifications": [
"cell line",
"multiplexed sample"
],
"creation_timestamp": "2024-07-22T00:26:42.800900+00:00",
"disease_terms": [],
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"status": "released"
},
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"status": "released"
},
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"status": "released"
},
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"status": "released"
}
],
"file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6521MNHG/",
"accession": "IGVFDS6521MNHG",
"aliases": [
"ansuman-satpathy:multiseq_igvf10_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"status": "released",
"summary": "lipid-conjugated oligo sequencing for interference single-nucleus ATAC-seq (10x multiome with MULTI-seq), interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
},
{
"@id": "/measurement-sets/IGVFDS1013HCXI/",
"accession": "IGVFDS1013HCXI",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf10_10x2"
],
"file_set_type": "experimental data",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released",
"summary": "interference single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
},
{
"@id": "/measurement-sets/IGVFDS9139TBCB/",
"accession": "IGVFDS9139TBCB",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf10_10x2"
],
"file_set_type": "experimental data",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released",
"summary": "interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
},
{
"@id": "/analysis-sets/IGVFDS2018URDY/",
"accession": "IGVFDS2018URDY",
"aliases": [
"ansuman-satpathy:igvf10_analysis_set"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
{
"@id": "/analysis-sets/IGVFDS5839UBFZ/",
"accession": "IGVFDS5839UBFZ",
"aliases": [
"ansuman-satpathy:IGVFDS1013HCXI_IGVFDS3910GBDQ_IGVFDS9139TBCB_IGVFDS2246RAZO_analysis",
"jesse-engreitz:IGVFDS1013HCXI_IGVFDS3910GBDQ_IGVFDS9139TBCB_IGVFDS2246RAZO_analysis"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "in progress",
"summary": "10x multiome with MULTI-seq"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"cas": "dCas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"fused_domain": "KOX1-KRAB",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"multiplexed_in": [],
"multiplexed_samples": [
{
"@id": "/in-vitro-systems/IGVFSM0962TVTG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0962TVTG",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/in-vitro-systems/IGVFSM6891FDIO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6891FDIO",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/in-vitro-systems/IGVFSM6228CZPK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6228CZPK",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9816PABB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9816PABB",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7325ZQQL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7325ZQQL",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM3274PSVP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3274PSVP",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM7537XJNH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7537XJNH",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens 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"
},
{
"@id": "/in-vitro-systems/IGVFSM0143DYAD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0143DYAD",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens 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"
},
{
"@id": "/in-vitro-systems/IGVFSM0387IPUP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0387IPUP",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB"
},
{
"@id": "/in-vitro-systems/IGVFSM7869DXPV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7869DXPV",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"multiplexing_methods": [
"barcode based"
],
"notes": "This object's multiplexing_methods has been set to barcode based by an upgrade. Please make sure it is correct before removing the notes.",
"origin_of": [],
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"release_timestamp": "2025-03-07T01:13:48.976348+00:00",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"schema_version": "10",
"sorted_fractions": [],
"sources": [
{
"@id": "/labs/jesse-engreitz/",
"status": "current",
"title": "Jesse Engreitz, Stanford"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"summary": "multiplexed sample: Jurkat cell line, male, Homo sapiens 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; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"depletion": false,
"purpose": "stimulation",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate",
"treatment_type": "chemical"
},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"depletion": false,
"purpose": "stimulation",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain",
"treatment_type": "protein"
}
],
"uuid": "22e9a8d0-c42c-4e31-8a81-14f8ba6a4fae",
"virtual": false
}