{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS3516UQYJ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3516UQYJ",
"aliases": [
"ali-mortazavi:igvf_015_Subpool_UDI26_total+core"
],
"assay_titles": [
"Parse SPLiT-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released multiplexed sample [IGVFSM2647QPOT](/multiplexed-samples/IGVFSM2647QPOT/) has in progress subobject tabular file [IGVFFI9660XHAT](/tabular-files/IGVFFI9660XHAT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/multiplexed-samples/IGVFSM2647QPOT/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM2647QPOT](/multiplexed-samples/IGVFSM2647QPOT/) 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/IGVFSM2647QPOT/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS3516UQYJ](/analysis-sets/IGVFDS3516UQYJ/) has `input_file_sets` with multiplexed samples: [IGVFSM2647QPOT](/multiplexed-samples/IGVFSM2647QPOT/) 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/IGVFDS3516UQYJ/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS3516UQYJ](/analysis-sets/IGVFDS3516UQYJ/) 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/IGVFDS3516UQYJ/"
},
{
"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": "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/"
}
]
},
"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": "2025-04-05T02:09:13.200221+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"description": "8 cube mouse founder strains plate igvf_015 Subpool_UDI26 with Cortex/Hippocampus, Diencephalon/Pituitary, Heart, Liver, Kidney, Gastrocnemius, Adrenal gland, Gonads, PBMC as the tissue",
"documents": [
"/documents/553bc3b9-0961-40aa-b099-27d0f17b2519/"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO8273JCQS/",
"accession": "IGVFDO8273JCQS",
"aliases": [
"ali-mortazavi:243_TREM2_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4735TLVS/",
"accession": "IGVFDO4735TLVS",
"aliases": [
"ali-mortazavi:250_TREM2_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6323XMSE/",
"accession": "IGVFDO6323XMSE",
"aliases": [
"ali-mortazavi:241_TREM2_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO9982CQID/",
"accession": "IGVFDO9982CQID",
"aliases": [
"ali-mortazavi:247_TREM2_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0308BSMU/",
"accession": "IGVFDO0308BSMU",
"aliases": [
"ali-mortazavi:239_TREM2_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7971CRWV/",
"accession": "IGVFDO7971CRWV",
"aliases": [
"ali-mortazavi:248_TREM2_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0326BOMZ/",
"accession": "IGVFDO0326BOMZ",
"aliases": [
"ali-mortazavi:245_TREM2_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO2081PBMC/",
"accession": "IGVFDO2081PBMC",
"aliases": [
"ali-mortazavi:240_TREM2_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO9500GYNY/",
"accession": "IGVFDO9500GYNY",
"aliases": [
"ali-mortazavi:244_TREM2_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4958MWGS/",
"accession": "IGVFDO4958MWGS",
"aliases": [
"ali-mortazavi:242_TREM2_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI4354MUBS/",
"accession": "IGVFFI4354MUBS",
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-04-06T23:13:13.753440+00:00",
"derived_from": [
"/sequence-files/IGVFFI9521KWMF/",
"/sequence-files/IGVFFI2033IHBM/",
"/sequence-files/IGVFFI8276TTCI/",
"/sequence-files/IGVFFI3978LEXD/"
],
"file_format": "tar",
"file_size": 958489689,
"href": "/matrix-files/IGVFFI4354MUBS/@@download/IGVFFI4354MUBS.tar.gz",
"md5sum": "3d8ee21fe5980ac56dd31fdf3f2500ff",
"s3_uri": "s3://igvf-files/2025/04/06/65effe05-4537-4ea2-8306-33618866ca22/IGVFFI4354MUBS.tar.gz",
"status": "released",
"submitted_file_name": "igvf_015/igvf_015_Subpool_UDI26_total+core.tar.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9604WYAS/",
"accession": "IGVFDS9604WYAS",
"aliases": [
"ali-mortazavi:015_67D_illumina"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [
"/analysis-sets/IGVFDS3307LCYV/",
"/analysis-sets/IGVFDS8922SXYI/",
"/analysis-sets/IGVFDS1969BPHC/",
"/analysis-sets/IGVFDS5270GNCH/",
"/analysis-sets/IGVFDS0262UVCA/",
"/analysis-sets/IGVFDS1854AUUI/",
"/analysis-sets/IGVFDS9802FTSJ/",
"/analysis-sets/IGVFDS8104ESQN/",
"/analysis-sets/IGVFDS7546DRSQ/",
"/analysis-sets/IGVFDS6994WJTF/"
],
"lab": {
"@id": "/labs/ali-mortazavi/",
"title": "Ali Mortazavi, UCI"
},
"protocols": [
"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-kxygx396zg8j/v2",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-n2bvj3noplk5/v2",
"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-36wgq3e3ylk5/v1",
"https://www.protocols.io/view/evercode-wt-mega-v2-2-1-8epv5xxrng1b/v1",
"https://www.protocols.io/view/evercode-dual-index-pcr-yxmvmeqe5g3p/v1",
"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-dm6gp3zedvzp/v2",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-14egn334ml5d/v2",
"https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-5qpvo3837v4o/v1"
],
"release_timestamp": "2025-04-19T04:50:09.558434+00:00",
"sample_summary": "Mus musculus multiplexed sample of adrenal gland, epididymis, gastrocnemius, heart, hypothalamus, kidney, left cerebral cortex, left hippocampal formation, liver, ovary, oviduct, peripheral blood mononuclear cell, pituitary gland, testis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2647QPOT/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2647QPOT",
"aliases": [
"ali-mortazavi:subpool_015_67D"
],
"cellular_sub_pool": "015_67D",
"classifications": [
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_2000001/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "peripheral blood mononuclear cell",
"term_name": "peripheral blood mononuclear cell"
},
{
"@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_0000473/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "testis",
"term_name": "testis"
},
{
"@id": "/sample-terms/UBERON_0000948/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "heart",
"term_name": "heart"
},
{
"@id": "/sample-terms/UBERON_0000992/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "ovary",
"term_name": "ovary"
},
{
"@id": "/sample-terms/UBERON_0000993/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "oviduct",
"term_name": "oviduct"
},
{
"@id": "/sample-terms/UBERON_0001301/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "epididymis",
"term_name": "epididymis"
},
{
"@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_0002107/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "liver",
"term_name": "liver"
},
{
"@id": "/sample-terms/UBERON_0002113/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "kidney",
"term_name": "kidney"
},
{
"@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 B6(SJL)-Trem2<em1Aduci>/J (female, 65 days) hypothalamus tissue; Mus musculus B6(SJL)-Trem2<em1Aduci>/J (male, 69 days) liver tissue; ... and 94 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": "2025-04-06T23:13:13.753440+00:00",
"summary": "Parse SPLiT-seq: sparse gene count matrix",
"uuid": "a619f550-4626-4581-a740-4da61b66253d",
"workflows": [
{
"@id": "/workflows/IGVFWF6241JYDF/",
"accession": "IGVFWF6241JYDF",
"name": "UCI snRNA-seq workflow",
"status": "released"
}
]
}