{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS2413FYLA/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2413FYLA",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_4"
],
"assay_titles": [
"Parse SPLiT-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"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/"
}
],
"WARNING": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS2413FYLA](/analysis-sets/IGVFDS2413FYLA/) has `input_file_sets` with multiplexed samples: [IGVFSM9603DIDI](/multiplexed-samples/IGVFSM9603DIDI/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
"level": 40,
"level_name": "WARNING",
"name": "audit_analysis_set_multiplexed_samples",
"path": "/analysis-sets/IGVFDS2413FYLA/"
}
]
},
"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": "2024-09-03T23:14:38.209643+00:00",
"description": "Lab processed snRNA-seq gene counts with clusters and cell type annotations for IGVF C57BL/6J and Castaneus left cortex bridge subpool 4",
"documents": [
"/documents/7c9b9828-5097-48cc-942c-e000579e7de4/"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO7361LABA/",
"accession": "IGVFDO7361LABA",
"aliases": [
"ali-mortazavi:118_B6J_10F"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4816HOFW/",
"accession": "IGVFDO4816HOFW",
"aliases": [
"ali-mortazavi:107_CASTJ_10M"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0493VGMC/",
"accession": "IGVFDO0493VGMC",
"aliases": [
"ali-mortazavi:108_CASTJ_10F"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO1486RZJK/",
"accession": "IGVFDO1486RZJK",
"aliases": [
"ali-mortazavi:105_CASTJ_10M"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO3261YWHI/",
"accession": "IGVFDO3261YWHI",
"aliases": [
"ali-mortazavi:119_B6J_10M"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO9333ACQP/",
"accession": "IGVFDO9333ACQP",
"aliases": [
"ali-mortazavi:120_B6J_10F"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6942KQBN/",
"accession": "IGVFDO6942KQBN",
"aliases": [
"ali-mortazavi:117_B6J_10M"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO8652OFEQ/",
"accession": "IGVFDO8652OFEQ",
"aliases": [
"ali-mortazavi:106_CASTJ_10F"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI6356ADHE/",
"accession": "IGVFFI6356ADHE",
"aliases": [
"ali-mortazavi:IGVF_B01_Subpool_4_total+core"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-09-03T23:39:15.789372+00:00",
"file_format": "tar",
"file_size": 413572778,
"href": "/matrix-files/IGVFFI6356ADHE/@@download/IGVFFI6356ADHE.tar.gz",
"s3_uri": "s3://igvf-files/2024/09/03/7dfa71d9-db7f-4478-89e9-141c1409e0bd/IGVFFI6356ADHE.tar.gz",
"submitted_file_name": "IGVF_B01_Subpool_4_total+core.tar.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI7274KDWO/",
"accession": "IGVFFI7274KDWO",
"aliases": [
"ali-mortazavi:IGVF_B01_Subpool_4_filtered_denoised"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-09-03T23:39:22.241639+00:00",
"file_format": "h5ad",
"file_size": 1098881208,
"href": "/matrix-files/IGVFFI7274KDWO/@@download/IGVFFI7274KDWO.h5ad",
"s3_uri": "s3://igvf-files/2024/09/03/01f11cf8-731c-4fb9-8388-2d6216902c66/IGVFFI7274KDWO.h5ad",
"submitted_file_name": "Subpool_4_filtered_adata_denoised.h5ad",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI2560RYCC/",
"accession": "IGVFFI2560RYCC",
"aliases": [
"ali-mortazavi:IGVF_B01_Subpool_4_total+core_replacement"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-10-09T20:53:57.724620+00:00",
"file_format": "tar",
"file_size": 413572800,
"href": "/matrix-files/IGVFFI2560RYCC/@@download/IGVFFI2560RYCC.tar.gz",
"s3_uri": "s3://igvf-files/2024/10/09/54c0f4bf-fc3d-4bc4-adfc-bc10ead0b9d4/IGVFFI2560RYCC.tar.gz",
"submitted_file_name": "IGVF_B01_Subpool_4_total+core.tar.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6946BUZB/",
"accession": "IGVFDS6946BUZB",
"aliases": [
"ali-mortazavi:B01_13D_illumina"
],
"file_set_type": "experimental data"
}
],
"input_for": [
"/analysis-sets/IGVFDS4883TFKC/"
],
"lab": {
"@id": "/labs/ali-mortazavi/",
"title": "Ali Mortazavi, UCI"
},
"notes": ". This analysis set previous specified samples: /tissues/IGVFSM7772DGMA/,/tissues/IGVFSM7094ZNGP/,/tissues/IGVFSM5782OIYL/,/tissues/IGVFSM5157GFSA/,/tissues/IGVFSM2279TQMZ/,/tissues/IGVFSM0447EABS/,/tissues/IGVFSM6969SYOD/,/tissues/IGVFSM3421UUOE/, but this property is now calculated through the input_file_sets.",
"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-cryopreser-4r3l22y2pl1y/v1",
"https://www.protocols.io/view/evercode-single-index-pcr-5jyl82k9rl2w/v1"
],
"release_timestamp": "2024-09-05T18:27:44.612637+00:00",
"sample_summary": "left cerebral cortex multiplexed sample",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9603DIDI/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9603DIDI",
"aliases": [
"ali-mortazavi:subpool_b01_13d"
],
"classifications": [
"multiplexed sample"
],
"construct_library_sets": [],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "multiplexed sample: left cerebral cortex tissue, female, Mus musculus CASTJ (72 days); left cerebral cortex tissue, male, Mus musculus B6J (72 days); ... and 6 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": "2024-09-03T23:39:15.789372+00:00",
"summary": "Parse SPLiT-seq: sparse gene count matrix",
"uuid": "19ec85c4-3071-47ce-b31f-eb3ed16da4e2",
"workflows": [
{
"@id": "/workflows/IGVFWF6241JYDF/",
"accession": "IGVFWF6241JYDF",
"name": "UCI snRNA-seq workflow"
}
]
}