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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9706KRLB](/measurement-sets/IGVFDS9706KRLB/) has sequence file(s): [IGVFFI3659ZCZH](/sequence-files/IGVFFI3659ZCZH/), [IGVFFI3996QJIG](/sequence-files/IGVFFI3996QJIG/), [IGVFFI8174OMEL](/sequence-files/IGVFFI8174OMEL/), [IGVFFI8877ARTC](/sequence-files/IGVFFI8877ARTC/), [IGVFFI7266BKEU](/sequence-files/IGVFFI7266BKEU/), [IGVFFI7442ZNAW](/sequence-files/IGVFFI7442ZNAW/), [IGVFFI6776RBKW](/sequence-files/IGVFFI6776RBKW/), [IGVFFI8406PONW](/sequence-files/IGVFFI8406PONW/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS9706KRLB/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9706KRLB](/measurement-sets/IGVFDS9706KRLB/) 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/IGVFDS9706KRLB/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS9706KRLB](/measurement-sets/IGVFDS9706KRLB/) 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_for",
"path": "/measurement-sets/IGVFDS9706KRLB/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2025-03-19T21:45:11.238801+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO4191KJBR/",
"accession": "IGVFDO4191KJBR",
"aliases": [
"igvf:corces_donor_BANN0129"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9211DWXZ/",
"accession": "IGVFDO9211DWXZ",
"aliases": [
"igvf:corces_donor_BANN1352"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO5718REZU/",
"accession": "IGVFDO5718REZU",
"aliases": [
"igvf:corces_donor_BANN9926"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7678VYKP/",
"accession": "IGVFDO7678VYKP",
"aliases": [
"igvf:corces_donor_BANN1235"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7815RLQM/",
"accession": "IGVFDO7815RLQM",
"aliases": [
"igvf:corces_donor_BANN1504"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4053HEKW/",
"accession": "IGVFDO4053HEKW",
"aliases": [
"igvf:corces_donor_BANN1317"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7387JZDV/",
"accession": "IGVFDO7387JZDV",
"aliases": [
"igvf:corces_donor_BANN1349"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2028IGVN/",
"accession": "IGVFDO2028IGVN",
"aliases": [
"igvf:corces_donor_BANN1256"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3659ZCZH/",
"accession": "IGVFFI3659ZCZH",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L005_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:00.585785+00:00",
"file_format": "fastq",
"file_size": 1137896048,
"href": "/sequence-files/IGVFFI3659ZCZH/@@download/IGVFFI3659ZCZH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/c2f032ec-6e28-400d-a436-ecc99fb9cb33/IGVFFI3659ZCZH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3996QJIG/",
"accession": "IGVFFI3996QJIG",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L006_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:21.078963+00:00",
"file_format": "fastq",
"file_size": 12150040540,
"href": "/sequence-files/IGVFFI3996QJIG/@@download/IGVFFI3996QJIG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/a2c911f6-b550-4fb5-9c2d-caf98ffb6e06/IGVFFI3996QJIG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8174OMEL/",
"accession": "IGVFFI8174OMEL",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:06.891197+00:00",
"file_format": "fastq",
"file_size": 11773607948,
"href": "/sequence-files/IGVFFI8174OMEL/@@download/IGVFFI8174OMEL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/e3c29af4-6a7d-48de-b596-23ca8335ff80/IGVFFI8174OMEL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8877ARTC/",
"accession": "IGVFFI8877ARTC",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L006_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:17.649014+00:00",
"file_format": "fastq",
"file_size": 16101331311,
"href": "/sequence-files/IGVFFI8877ARTC/@@download/IGVFFI8877ARTC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/dc73e251-6638-43cc-bebe-c90b57f6af1e/IGVFFI8877ARTC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7266BKEU/",
"accession": "IGVFFI7266BKEU",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L005_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:15:57.293735+00:00",
"file_format": "fastq",
"file_size": 1221511077,
"href": "/sequence-files/IGVFFI7266BKEU/@@download/IGVFFI7266BKEU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/dd1ec932-2422-4dab-a796-d22f71c3a12f/IGVFFI7266BKEU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7442ZNAW/",
"accession": "IGVFFI7442ZNAW",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:03.761766+00:00",
"file_format": "fastq",
"file_size": 15685581087,
"href": "/sequence-files/IGVFFI7442ZNAW/@@download/IGVFFI7442ZNAW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/6ebcb02c-729c-4b4f-8800-7a5421805bc3/IGVFFI7442ZNAW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6776RBKW/",
"accession": "IGVFFI6776RBKW",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L006_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:10.401503+00:00",
"file_format": "fastq",
"file_size": 1260408915,
"href": "/sequence-files/IGVFFI6776RBKW/@@download/IGVFFI6776RBKW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/4ab0d548-2c8f-46b5-b178-18a7c67fe6a3/IGVFFI6776RBKW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8406PONW/",
"accession": "IGVFFI8406PONW",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G8_P076_L006_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:16:13.907852+00:00",
"file_format": "fastq",
"file_size": 1174460011,
"href": "/sequence-files/IGVFFI8406PONW/@@download/IGVFFI8406PONW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/b55115ad-5643-47b2-b94b-6f1222cb463e/IGVFFI8406PONW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G8_L008_P076_S48_L006_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ryan-corces/",
"title": "Ryan Corces, Gladstone Institute UCSF"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI8751YQRY/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome",
"protocols": [
"https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS7070YJKH/",
"accession": "IGVFDS7070YJKH",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2979ZZFZ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2979ZZFZ",
"aliases": [
"igvf:corces_multiplexedSample_RP026_G8"
],
"classifications": [
"tissue",
"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/DOID_0080832/",
"status": "in progress",
"term_name": "mild cognitive impairment"
},
{
"@id": "/phenotype-terms/DOID_14330/",
"status": "in progress",
"term_name": "Parkinson's disease"
},
{
"@id": "/phenotype-terms/DOID_9246/",
"status": "in progress",
"term_name": "cerebral amyloid angiopathy"
},
{
"@id": "/phenotype-terms/MONDO_0004975/",
"status": "released",
"term_name": "Alzheimer disease"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
"certificate_identifier": "IP115-05",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001874/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "putamen",
"term_name": "putamen"
},
{
"@id": "/sample-terms/UBERON_0002038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "substantia nigra",
"term_name": "substantia nigra"
},
{
"@id": "/sample-terms/UBERON_0002740/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "posterior cingulate gyrus",
"term_name": "posterior cingulate gyrus"
},
{
"@id": "/sample-terms/UBERON_0002771/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "middle temporal gyrus",
"term_name": "middle temporal gyrus"
}
],
"status": "preview",
"summary": "multiplexed sample: Homo sapiens (female, 72 years) posterior cingulate gyrus tissue associated with Parkinson's disease; Homo sapiens (female, 79 years) middle temporal gyrus tissue associated with Parkinson's disease; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-21T00:15:57.293735+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "77b92b92-bd0e-4e07-80ea-5dd629135337"
}