{
"@context": "/terms/",
"@id": "/multiplexed-samples/IGVFSM3762JDVU/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM3762JDVU",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf12_10x4"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4605UDLV](/in-vitro-systems/IGVFSM4605UDLV/) 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": "/in-vitro-systems/IGVFSM4605UDLV/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3775ZYEG](/in-vitro-systems/IGVFSM3775ZYEG/) 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": "/in-vitro-systems/IGVFSM3775ZYEG/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0423ICBM](/in-vitro-systems/IGVFSM0423ICBM/) 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": "/in-vitro-systems/IGVFSM0423ICBM/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM7378CNYR](/tissues/IGVFSM7378CNYR/) 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": "/tissues/IGVFSM7378CNYR/"
},
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM7378CNYR](/tissues/IGVFSM7378CNYR/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_tissue_ccf_id",
"path": "/tissues/IGVFSM7378CNYR/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7661FMCI](/in-vitro-systems/IGVFSM7661FMCI/) 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": "/in-vitro-systems/IGVFSM7661FMCI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7102SSKB](/in-vitro-systems/IGVFSM7102SSKB/) 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": "/in-vitro-systems/IGVFSM7102SSKB/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4177YLPO](/in-vitro-systems/IGVFSM4177YLPO/) 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": "/in-vitro-systems/IGVFSM4177YLPO/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0576KKQT](/in-vitro-systems/IGVFSM0576KKQT/) 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": "/in-vitro-systems/IGVFSM0576KKQT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8141PBNS](/in-vitro-systems/IGVFSM8141PBNS/) 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": "/in-vitro-systems/IGVFSM8141PBNS/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM2973LYHI](/tissues/IGVFSM2973LYHI/) 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": "/tissues/IGVFSM2973LYHI/"
},
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM2973LYHI](/tissues/IGVFSM2973LYHI/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_tissue_ccf_id",
"path": "/tissues/IGVFSM2973LYHI/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9845AOVZ](/in-vitro-systems/IGVFSM9845AOVZ/) 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": "/in-vitro-systems/IGVFSM9845AOVZ/"
},
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM3762JDVU](/multiplexed-samples/IGVFSM3762JDVU/) has in progress subobject tabular file [IGVFFI6870GMPP](/tabular-files/IGVFFI6870GMPP/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM3762JDVU/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM3762JDVU](/multiplexed-samples/IGVFSM3762JDVU/) 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/IGVFSM3762JDVU/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2173XZZU](/in-vitro-systems/IGVFSM2173XZZU/) 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": "/in-vitro-systems/IGVFSM2173XZZU/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping"
},
"barcode_map": "/tabular-files/IGVFFI6870GMPP/",
"biomarkers": [],
"classifications": [
"differentiated cell specimen",
"tissue",
"multiplexed sample"
],
"creation_timestamp": "2024-07-23T20:58:33.633789+00:00",
"disease_terms": [],
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"ethnicities": [
"European"
],
"status": "released"
},
{
"@id": "/human-donors/IGVFDO1264SGCS/",
"accession": "IGVFDO1264SGCS",
"ethnicities": [
"African American"
],
"status": "released"
},
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"ethnicities": [
"African American"
],
"status": "released"
}
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS2361VFLK/",
"accession": "IGVFDS2361VFLK",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf12_10x4"
],
"file_set_type": "experimental data",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released",
"summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
},
{
"@id": "/auxiliary-sets/IGVFDS5974ACGH/",
"accession": "IGVFDS5974ACGH",
"aliases": [
"ansuman-satpathy:multiseq_igvf12_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"status": "released",
"summary": "lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
},
{
"@id": "/measurement-sets/IGVFDS5103JQSX/",
"accession": "IGVFDS5103JQSX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf12_10x4"
],
"file_set_type": "experimental data",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
},
{
"@id": "/analysis-sets/IGVFDS4731QGJR/",
"accession": "IGVFDS4731QGJR",
"aliases": [
"ansuman-satpathy:igvf12_analysis_set_10x4"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Ansuman Satpathy, Stanford"
},
"status": "released",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq): cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/1e03eda3-a983-4cee-864e-43acb4c1b186/",
"certificate_identifier": "IP115-18",
"controlled_access": true,
"data_use_limitation": "GRU",
"data_use_limitation_summary": "GRU",
"status": "released"
},
{
"@id": "/institutional-certificates/460c2060-3b32-43c1-ab4b-b2ef0fbeb2b2/",
"certificate_identifier": "IP115-22",
"controlled_access": true,
"data_use_limitation": "GRU",
"data_use_limitation_summary": "GRU",
"status": "released"
}
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"modifications": [],
"multiplexed_in": [],
"multiplexed_samples": [
{
"@id": "/in-vitro-systems/IGVFSM8141PBNS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8141PBNS",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen"
},
{
"@id": "/in-vitro-systems/IGVFSM3775ZYEG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3775ZYEG",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 1 day"
},
{
"@id": "/in-vitro-systems/IGVFSM9845AOVZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9845AOVZ",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 2 days"
},
{
"@id": "/in-vitro-systems/IGVFSM4177YLPO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4177YLPO",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 3 days"
},
{
"@id": "/in-vitro-systems/IGVFSM2173XZZU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2173XZZU",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 4 days"
},
{
"@id": "/in-vitro-systems/IGVFSM0576KKQT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0576KKQT",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days"
},
{
"@id": "/in-vitro-systems/IGVFSM0423ICBM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0423ICBM",
"donors": [
{
"@id": "/human-donors/IGVFDO0938OYMI/",
"accession": "IGVFDO0938OYMI",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days"
},
{
"@id": "/in-vitro-systems/IGVFSM7661FMCI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7661FMCI",
"donors": [
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (male) B differentiated cell specimen"
},
{
"@id": "/in-vitro-systems/IGVFSM7102SSKB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7102SSKB",
"donors": [
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 5 days"
},
{
"@id": "/in-vitro-systems/IGVFSM4605UDLV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4605UDLV",
"donors": [
{
"@id": "/human-donors/IGVFDO1718HCES/",
"accession": "IGVFDO1718HCES",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
}
],
"status": "released",
"summary": "Homo sapiens (male) B differentiated cell specimen induced to plasmablast for 6 days"
},
{
"@id": "/tissues/IGVFSM2973LYHI/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2973LYHI",
"donors": [
{
"@id": "/human-donors/IGVFDO1264SGCS/",
"accession": "IGVFDO1264SGCS",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002371/",
"status": "released",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "Homo sapiens (male, 44 years) bone marrow tissue"
},
{
"@id": "/tissues/IGVFSM7378CNYR/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7378CNYR",
"donors": [
{
"@id": "/human-donors/IGVFDO1264SGCS/",
"accession": "IGVFDO1264SGCS",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002371/",
"status": "released",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "Homo sapiens (male, 44 years) bone marrow tissue"
}
],
"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": "2025-03-22T00:38:26.211821+00:00",
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
},
{
"@id": "/sample-terms/UBERON_0002371/",
"status": "released",
"term_name": "bone marrow"
}
],
"schema_version": "10",
"sorted_fractions": [],
"sources": [
{
"@id": "/labs/bradley-bernstein/",
"status": "current",
"title": "Bradley Bernstein, Broad"
},
{
"@id": "/labs/harinder-singh/",
"status": "current",
"title": "Harinder Singh, University of Pittsburgh"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": [],
"uuid": "181eb835-3c2c-4832-a7cd-53a8dc425cab",
"virtual": false
}