{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4803WKTQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4803WKTQ",
"aliases": [
"ali-mortazavi:B01_13G_nanopore"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"term_name": "single-nucleus RNA sequencing assay"
},
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4803WKTQ](/measurement-sets/IGVFDS4803WKTQ/) has sequence file(s): [IGVFFI3397RQUC](/sequence-files/IGVFFI3397RQUC/), [IGVFFI2224QAWI](/sequence-files/IGVFFI2224QAWI/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS4803WKTQ/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS4803WKTQ](/measurement-sets/IGVFDS4803WKTQ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/measurement-sets/IGVFDS4803WKTQ/"
}
]
},
"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": "2024-04-29T18:59:22.864605+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO7361LABA/",
"accession": "IGVFDO7361LABA",
"aliases": [
"ali-mortazavi:118_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/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/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/IGVFDO1486RZJK/",
"accession": "IGVFDO1486RZJK",
"aliases": [
"ali-mortazavi:105_CASTJ_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": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3397RQUC/",
"accession": "IGVFFI3397RQUC",
"aliases": [
"ali-mortazavi:igvfB01_13G-gc_lig-ss_11.pod5"
],
"content_type": "Nanopore reads",
"creation_timestamp": "2024-04-30T16:55:40.126406+00:00",
"file_format": "pod5",
"file_size": 1141803266280,
"href": "/sequence-files/IGVFFI3397RQUC/@@download/IGVFFI3397RQUC.pod5",
"s3_uri": "s3://igvf-files/2024/04/30/c6bec196-fe41-4d46-977b-1f31a8a72edf/IGVFFI3397RQUC.pod5",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0700019/",
"term_name": "ONT PromethION 2 Solo"
},
"submitted_file_name": "igvf_b01/nanopore_p2/igvfb01_13G-gc_lig-ss_11.pod5",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2224QAWI/",
"accession": "IGVFFI2224QAWI",
"content_type": "reads",
"creation_timestamp": "2024-05-01T02:08:54.793631+00:00",
"file_format": "fastq",
"file_size": 83297971550,
"href": "/sequence-files/IGVFFI2224QAWI/@@download/IGVFFI2224QAWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/05/01/bc97e654-08b3-4533-b167-077ed920532f/IGVFFI2224QAWI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0700019/",
"term_name": "ONT PromethION 2 Solo"
},
"submitted_file_name": "igvf_b01/nanopore_p2/igvfb01_13G-gc_lig-ss_11.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/ali-mortazavi/",
"title": "Ali Mortazavi, UCI"
},
"preferred_assay_title": "Parse SPLiT-seq",
"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/cdna-exome-capture-v1-0-1-36wgq3b83lk5/v1",
"https://www.protocols.io/view/ont-library-prep-for-split-seq-cdna-eq2lyj1xmlx9/v1"
],
"release_timestamp": "2024-05-08T23:38:43.026570+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8722YQAW/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8722YQAW",
"aliases": [
"ali-mortazavi:subpool_b01_13g"
],
"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",
"treatments": []
}
],
"schema_version": "21",
"sequencing_library_types": [
"exome capture"
],
"status": "released",
"submitted_by": {
"@id": "/users/ebd1025b-e3ab-4e51-bfcd-1415f278281a/",
"title": "Diane Trout"
},
"submitted_files_timestamp": "2024-04-30T16:55:40.126406+00:00",
"summary": "Parse SPLiT-seq",
"uuid": "4a15cf9b-b172-4b42-bf9b-eb52600b7605"
}