{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5380YBJA/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5380YBJA",
"aliases": [
"ali-mortazavi:igvf_012_Subpool_7_total+core"
],
"assay_titles": [
"Parse SPLiT-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000750](/sample-terms/NTR_0000750/) 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_0000750/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) 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_0000646/"
},
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM7258KMGW](/multiplexed-samples/IGVFSM7258KMGW/) has in progress subobject tabular file [IGVFFI7516EHMR](/tabular-files/IGVFFI7516EHMR/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM7258KMGW/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM7258KMGW](/multiplexed-samples/IGVFSM7258KMGW/) 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/IGVFSM7258KMGW/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS5380YBJA](/analysis-sets/IGVFDS5380YBJA/) has `input_file_sets` with multiplexed samples: [IGVFSM7258KMGW](/multiplexed-samples/IGVFSM7258KMGW/) 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/IGVFDS5380YBJA/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS5380YBJA](/analysis-sets/IGVFDS5380YBJA/) 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/IGVFDS5380YBJA/"
}
]
},
"award": {
"@id": "/awards/HG012077/",
"component": "mapping",
"contact_pi": {
"@id": "/users/2c33e192-e815-4384-a220-72a0992cbe24/",
"title": "Ali Mortazavi"
},
"title": "Center for Mouse Genomic Variation at Single Cell Resolution"
},
"control_for": [],
"creation_timestamp": "2025-04-05T02:09:07.611462+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"description": "8 cube mouse founder strains plate igvf_012 Subpool_7 with mixed tissues",
"documents": [
"/documents/e5f20ba9-f4d9-4811-890a-520031059d0b/"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO3762EAWT/",
"accession": "IGVFDO3762EAWT",
"aliases": [
"ali-mortazavi:076_PWKJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "PWK/PhJ (PWK)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7824YAWC/",
"accession": "IGVFDO7824YAWC",
"aliases": [
"ali-mortazavi:022_B6J_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO3534MDFF/",
"accession": "IGVFDO3534MDFF",
"aliases": [
"ali-mortazavi:046_NZOJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "NZO/H1LtJ (NZO)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO5539RLXJ/",
"accession": "IGVFDO5539RLXJ",
"aliases": [
"ali-mortazavi:029_AJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "A/J (AJ)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0853BCOL/",
"accession": "IGVFDO0853BCOL",
"aliases": [
"ali-mortazavi:058_WSBJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "WSB/EiJ (WSB)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0696DMIA/",
"accession": "IGVFDO0696DMIA",
"aliases": [
"ali-mortazavi:057_WSBJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "WSB/EiJ (WSB)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7255VZBN/",
"accession": "IGVFDO7255VZBN",
"aliases": [
"ali-mortazavi:062_WSBJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "WSB/EiJ (WSB)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7658MAGX/",
"accession": "IGVFDO7658MAGX",
"aliases": [
"ali-mortazavi:122_B6J_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7007WBAX/",
"accession": "IGVFDO7007WBAX",
"aliases": [
"ali-mortazavi:016_B6J_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7254QNQZ/",
"accession": "IGVFDO7254QNQZ",
"aliases": [
"ali-mortazavi:031_AJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "A/J (AJ)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO8958JQIY/",
"accession": "IGVFDO8958JQIY",
"aliases": [
"ali-mortazavi:047_NZOJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "NZO/H1LtJ (NZO)",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI8676NBKL/",
"accession": "IGVFFI8676NBKL",
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-04-06T23:12:47.934784+00:00",
"derived_from": [
"/sequence-files/IGVFFI2291OIKM/",
"/sequence-files/IGVFFI8601YVUZ/",
"/sequence-files/IGVFFI7572RVHD/",
"/sequence-files/IGVFFI3832VEJD/"
],
"file_format": "tar",
"file_size": 151293133,
"href": "/matrix-files/IGVFFI8676NBKL/@@download/IGVFFI8676NBKL.tar.gz",
"md5sum": "1ad19955d7f35013e83ad00cef534328",
"s3_uri": "s3://igvf-files/2025/04/06/faa25139-7bc8-485d-a68f-bd283f790843/IGVFFI8676NBKL.tar.gz",
"status": "released",
"submitted_file_name": "igvf_012/igvf_012_Subpool_7_total+core.tar.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5939OGHF/",
"accession": "IGVFDS5939OGHF",
"aliases": [
"ali-mortazavi:012_13G_illumina"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [
"/analysis-sets/IGVFDS8997QHCM/",
"/analysis-sets/IGVFDS2950ZMLN/",
"/analysis-sets/IGVFDS1666GZSV/",
"/analysis-sets/IGVFDS9423ZPAY/",
"/analysis-sets/IGVFDS0868APKJ/"
],
"lab": {
"@id": "/labs/ali-mortazavi/",
"title": "Ali Mortazavi, UCI"
},
"protocols": [
"https://www.protocols.io/view/evercode-wt-v2-2-1-eq2lyj9relx9/v1",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-n92ldm8b8l5b/v2",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-dm6gp3zedvzp/v2",
"https://www.protocols.io/view/evercode-single-index-pcr-5jyl82k9rl2w/v1",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-81wgbxzdylpk/v2",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-eq2lyj17rlx9/v1",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-n2bvj3noplk5/v2"
],
"release_timestamp": "2025-04-19T18:10:56.908685+00:00",
"sample_summary": "Mus musculus multiplexed sample of adrenal gland, gastrocnemius, heart, hypothalamus, left cerebral cortex, left hippocampal formation, pituitary gland",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7258KMGW/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7258KMGW",
"aliases": [
"ali-mortazavi:subpool_012_13G"
],
"cellular_sub_pool": "012_13G",
"classifications": [
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
},
{
"@id": "/sample-terms/NTR_0000750/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left hippocampal formation",
"term_name": "left hippocampal formation"
},
{
"@id": "/sample-terms/UBERON_0000007/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "pituitary gland",
"term_name": "pituitary gland"
},
{
"@id": "/sample-terms/UBERON_0000948/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "heart",
"term_name": "heart"
},
{
"@id": "/sample-terms/UBERON_0001388/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "gastrocnemius",
"term_name": "gastrocnemius"
},
{
"@id": "/sample-terms/UBERON_0001898/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "hypothalamus",
"term_name": "hypothalamus"
},
{
"@id": "/sample-terms/UBERON_0002369/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "adrenal gland",
"term_name": "adrenal gland"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus WSB/EiJ (male, 69 days) heart tissue; Mus musculus NZO/H1LtJ (female, 69 days) left cerebral cortex tissue; ... and 12 more samples",
"taxa": "Mus musculus",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/ebd1025b-e3ab-4e51-bfcd-1415f278281a/",
"title": "Diane Trout"
},
"submitted_files_timestamp": "2025-04-06T23:12:47.934784+00:00",
"summary": "Parse SPLiT-seq: sparse gene count matrix",
"uuid": "840b9495-7b1d-40ee-be55-ce4752901a9c",
"workflows": [
{
"@id": "/workflows/IGVFWF6241JYDF/",
"accession": "IGVFWF6241JYDF",
"name": "UCI snRNA-seq workflow",
"status": "released"
}
]
}