{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6946BUZB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6946BUZB",
"aliases": [
"ali-mortazavi:B01_13D_illumina"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"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": "Measurement set [IGVFDS6946BUZB](/measurement-sets/IGVFDS6946BUZB/) 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": "/measurement-sets/IGVFDS6946BUZB/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6946BUZB](/measurement-sets/IGVFDS6946BUZB/) has in progress subobject tabular file [IGVFFI1138MCVX](/tabular-files/IGVFFI1138MCVX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6946BUZB/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6946BUZB](/measurement-sets/IGVFDS6946BUZB/) has in progress subobject tabular file [IGVFFI0924TKJO](/tabular-files/IGVFFI0924TKJO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6946BUZB/"
},
{
"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 strand specificity",
"detail": "Measurement set [IGVFDS6946BUZB](/measurement-sets/IGVFDS6946BUZB/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS6946BUZB/"
}
]
},
"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": "2023-08-25T17:26:23.342732+00:00",
"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/IGVFDO0493VGMC/",
"accession": "IGVFDO0493VGMC",
"aliases": [
"ali-mortazavi:108_CASTJ_10F"
],
"sex": "female",
"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/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/IGVFDO9333ACQP/",
"accession": "IGVFDO9333ACQP",
"aliases": [
"ali-mortazavi:120_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"
},
{
"@id": "/rodent-donors/IGVFDO7361LABA/",
"accession": "IGVFDO7361LABA",
"aliases": [
"ali-mortazavi:118_B6J_10F"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2185ZXQY/",
"accession": "IGVFFI2185ZXQY",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-25T22:11:32.474396+00:00",
"file_format": "fastq",
"file_size": 6674177945,
"href": "/sequence-files/IGVFFI2185ZXQY/@@download/IGVFFI2185ZXQY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/25/c9c3c559-3689-4e8d-84f5-fd71c6dfe551/IGVFFI2185ZXQY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "igvf_b01/next1/igvf_b01_B04_D_next_N1_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5598BXFK/",
"accession": "IGVFFI5598BXFK",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-25T22:36:41.361643+00:00",
"file_format": "fastq",
"file_size": 7070087384,
"href": "/sequence-files/IGVFFI5598BXFK/@@download/IGVFFI5598BXFK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/25/822b11ba-1943-4be7-bbcb-188d88720117/IGVFFI5598BXFK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "igvf_b01/next2/igvf_b01_B04_D_next_N2_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4373RWTV/",
"accession": "IGVFFI4373RWTV",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-25T21:56:16.917963+00:00",
"file_format": "fastq",
"file_size": 12304437794,
"href": "/sequence-files/IGVFFI4373RWTV/@@download/IGVFFI4373RWTV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/25/062bc669-056f-446e-acee-fd170ba945d2/IGVFFI4373RWTV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "igvf_b01/next1/igvf_b01_B04_D_next_N1_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4299WSBH/",
"accession": "IGVFFI4299WSBH",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-25T22:19:54.416459+00:00",
"file_format": "fastq",
"file_size": 12630121291,
"href": "/sequence-files/IGVFFI4299WSBH/@@download/IGVFFI4299WSBH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/25/45082e7d-c1d2-48e5-b092-66a43a8d9f52/IGVFFI4299WSBH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "igvf_b01/next2/igvf_b01_B04_D_next_N2_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5693YBRI/",
"accession": "IGVFFI5693YBRI",
"content_type": "seqspec",
"creation_timestamp": "2024-08-30T21:35:19.855715+00:00",
"file_format": "yaml",
"file_size": 1345,
"href": "/configuration-files/IGVFFI5693YBRI/@@download/IGVFFI5693YBRI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/30/89c8631d-da9a-4e13-8c74-03ea549c9cf4/IGVFFI5693YBRI.yaml.gz",
"status": "in progress",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7226TLUF/",
"accession": "IGVFFI7226TLUF",
"content_type": "seqspec",
"creation_timestamp": "2024-08-30T21:35:21.315880+00:00",
"file_format": "yaml",
"file_size": 1345,
"href": "/configuration-files/IGVFFI7226TLUF/@@download/IGVFFI7226TLUF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/30/c2254723-1de9-4b13-814f-31cfb27ba2ca/IGVFFI7226TLUF.yaml.gz",
"status": "in progress",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2413FYLA/",
"/analysis-sets/IGVFDS5312WURZ/",
"/analysis-sets/IGVFDS5242HJOY/"
],
"lab": {
"@id": "/labs/ali-mortazavi/",
"title": "Ali Mortazavi, UCI"
},
"notes": "Preferred_assay_titles enum Parse Split-seq has been renamed to be Parse SPLiT-seq.",
"onlist_files": [
"/tabular-files/IGVFFI1138MCVX/",
"/tabular-files/IGVFFI0924TKJO/"
],
"onlist_method": "multi",
"preferred_assay_title": "Parse SPLiT-seq",
"protocols": [
"https://www.protocols.io/view/evercode-single-index-pcr-5jyl82k9rl2w/v1",
"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"
],
"release_timestamp": "2024-05-08T23:38:39.235003+00:00",
"samples": [
{
"@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": []
}
],
"schema_version": "26",
"sequencing_library_types": [
"mRNA enriched"
],
"status": "released",
"submitted_by": {
"@id": "/users/ebd1025b-e3ab-4e51-bfcd-1415f278281a/",
"title": "Diane Trout"
},
"submitted_files_timestamp": "2023-08-25T21:56:16.917963+00:00",
"summary": "Parse SPLiT-seq",
"uuid": "2eac7b48-46ab-4e54-afae-b05d4effd98e"
}