{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4883TFKC/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4883TFKC",
"aliases": [
"ali-mortazavi:IGVF_B01_LeftCortex"
],
"assay_titles": [
"Parse SPLiT-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM6546CQJB](/multiplexed-samples/IGVFSM6546CQJB/) 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/IGVFSM6546CQJB/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4883TFKC](/analysis-sets/IGVFDS4883TFKC/) has `input_file_sets` with multiplexed samples: [IGVFSM1955RVUC](/multiplexed-samples/IGVFSM1955RVUC/), [IGVFSM8093RPKR](/multiplexed-samples/IGVFSM8093RPKR/), [IGVFSM9603DIDI](/multiplexed-samples/IGVFSM9603DIDI/), [IGVFSM6546CQJB](/multiplexed-samples/IGVFSM6546CQJB/), [IGVFSM2294BOOU](/multiplexed-samples/IGVFSM2294BOOU/), [IGVFSM6958ESMJ](/multiplexed-samples/IGVFSM6958ESMJ/), [IGVFSM8722YQAW](/multiplexed-samples/IGVFSM8722YQAW/), [IGVFSM1676SYRC](/multiplexed-samples/IGVFSM1676SYRC/) 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/IGVFDS4883TFKC/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4883TFKC](/analysis-sets/IGVFDS4883TFKC/) 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/IGVFDS4883TFKC/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8093RPKR](/multiplexed-samples/IGVFSM8093RPKR/) 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/IGVFSM8093RPKR/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM9603DIDI](/multiplexed-samples/IGVFSM9603DIDI/) 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/IGVFSM9603DIDI/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM1955RVUC](/multiplexed-samples/IGVFSM1955RVUC/) 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/IGVFSM1955RVUC/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM1676SYRC](/multiplexed-samples/IGVFSM1676SYRC/) 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/IGVFSM1676SYRC/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM6958ESMJ](/multiplexed-samples/IGVFSM6958ESMJ/) 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/IGVFSM6958ESMJ/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8722YQAW](/multiplexed-samples/IGVFSM8722YQAW/) 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/IGVFSM8722YQAW/"
},
{
"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": "missing publication",
"detail": "Multiplexed sample [IGVFSM2294BOOU](/multiplexed-samples/IGVFSM2294BOOU/) 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/IGVFSM2294BOOU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Matrix file [IGVFFI5345SNRS](/matrix-files/IGVFFI5345SNRS/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_file_no_file_format_specifications",
"path": "/matrix-files/IGVFFI5345SNRS/"
}
]
},
"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": "2024-09-03T23:27:47.747055+00:00",
"description": "Lab processed snRNA-seq gene counts with clusters and cell type annotations for IGVF C57BL/6J and Castaneus left cortex bridge samples",
"documents": [
"/documents/49860adc-0f7d-4373-85dc-52604fcbbb1a/"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO3261YWHI/",
"accession": "IGVFDO3261YWHI",
"aliases": [
"ali-mortazavi:119_B6J_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4816HOFW/",
"accession": "IGVFDO4816HOFW",
"aliases": [
"ali-mortazavi:107_CASTJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO1486RZJK/",
"accession": "IGVFDO1486RZJK",
"aliases": [
"ali-mortazavi:105_CASTJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6942KQBN/",
"accession": "IGVFDO6942KQBN",
"aliases": [
"ali-mortazavi:117_B6J_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0493VGMC/",
"accession": "IGVFDO0493VGMC",
"aliases": [
"ali-mortazavi:108_CASTJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO9333ACQP/",
"accession": "IGVFDO9333ACQP",
"aliases": [
"ali-mortazavi:120_B6J_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7361LABA/",
"accession": "IGVFDO7361LABA",
"aliases": [
"ali-mortazavi:118_B6J_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO8652OFEQ/",
"accession": "IGVFDO8652OFEQ",
"aliases": [
"ali-mortazavi:106_CASTJ_10F"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI5345SNRS/",
"accession": "IGVFFI5345SNRS",
"aliases": [
"ali-mortazavi:IGVF_B01_LeftCortex_anndata"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2024-09-03T23:40:57.043264+00:00",
"file_format": "h5ad",
"file_size": 7066756745,
"href": "/matrix-files/IGVFFI5345SNRS/@@download/IGVFFI5345SNRS.h5ad",
"s3_uri": "s3://igvf-files/2024/09/03/60005c1e-96ac-4e2a-ae69-021e93a72106/IGVFFI5345SNRS.h5ad",
"status": "released",
"submitted_file_name": "IGVFB01_LeftCortex_annotated_adata.h5ad",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/analysis-sets/IGVFDS9520PLLU/",
"accession": "IGVFDS9520PLLU",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_1"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS7323SUVK/",
"accession": "IGVFDS7323SUVK",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_2"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS0223KLTB/",
"accession": "IGVFDS0223KLTB",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_3"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS2413FYLA/",
"accession": "IGVFDS2413FYLA",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_4"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS2762DTQI/",
"accession": "IGVFDS2762DTQI",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_5"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS3636WTST/",
"accession": "IGVFDS3636WTST",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_6"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS5115IZVN/",
"accession": "IGVFDS5115IZVN",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_7"
],
"file_set_type": "intermediate analysis",
"status": "released"
},
{
"@id": "/analysis-sets/IGVFDS8648GJCE/",
"accession": "IGVFDS8648GJCE",
"aliases": [
"ali-mortazavi:IGVF_B01_subpool_8"
],
"file_set_type": "intermediate analysis",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ali-mortazavi/",
"title": "Ali Mortazavi, UCI"
},
"protocols": [],
"release_timestamp": "2024-09-05T18:27:41.473484+00:00",
"sample_summary": "Mus musculus multiplexed sample of left cerebral cortex",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM1955RVUC/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1955RVUC",
"aliases": [
"ali-mortazavi:subpool_b01_13b"
],
"cellular_sub_pool": "B01_13B",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM8093RPKR/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8093RPKR",
"aliases": [
"ali-mortazavi:subpool_b01_13c"
],
"cellular_sub_pool": "B01_13C",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM9603DIDI/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9603DIDI",
"aliases": [
"ali-mortazavi:subpool_b01_13d"
],
"cellular_sub_pool": "B01_13D",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM6546CQJB/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6546CQJB",
"aliases": [
"ali-mortazavi:subpool_b01_13f"
],
"cellular_sub_pool": "B01_13F",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM2294BOOU/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2294BOOU",
"aliases": [
"ali-mortazavi:subpool_b01_13h"
],
"cellular_sub_pool": "B01_13H",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM6958ESMJ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6958ESMJ",
"aliases": [
"ali-mortazavi:subpool_b01_13e"
],
"cellular_sub_pool": "B01_13E",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM8722YQAW/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8722YQAW",
"aliases": [
"ali-mortazavi:subpool_b01_13g"
],
"cellular_sub_pool": "B01_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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... and 6 more samples",
"taxa": "Mus musculus",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM1676SYRC/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1676SYRC",
"aliases": [
"ali-mortazavi:subpool_b01_13a"
],
"cellular_sub_pool": "B01_13A",
"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"
}
],
"status": "released",
"summary": "multiplexed sample: Mus musculus CAST/EiJ (female, 72 days) left cerebral cortex tissue; Mus musculus C57BL/6J (male, 72 days) left cerebral cortex tissue; ... 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": "2024-09-03T23:40:57.043264+00:00",
"summary": "Parse SPLiT-seq: sparse gene count matrix",
"uuid": "a036861e-a44b-44e8-a904-138f3b8af431",
"workflows": [
{
"@id": "/workflows/IGVFWF6241JYDF/",
"accession": "IGVFWF6241JYDF",
"name": "UCI snRNA-seq workflow",
"status": "released"
}
]
}