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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5927HVQQ](/measurement-sets/IGVFDS5927HVQQ/) has sequence file(s): [IGVFFI7942OOZA](/sequence-files/IGVFFI7942OOZA/), [IGVFFI1204NCRP](/sequence-files/IGVFFI1204NCRP/), [IGVFFI8700OUUX](/sequence-files/IGVFFI8700OUUX/), [IGVFFI6746RQKD](/sequence-files/IGVFFI6746RQKD/), [IGVFFI2067XVHB](/sequence-files/IGVFFI2067XVHB/), [IGVFFI3601OLPT](/sequence-files/IGVFFI3601OLPT/), [IGVFFI1203RCNN](/sequence-files/IGVFFI1203RCNN/), [IGVFFI6029OWVO](/sequence-files/IGVFFI6029OWVO/) 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/IGVFDS5927HVQQ/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5927HVQQ](/measurement-sets/IGVFDS5927HVQQ/) 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/IGVFDS5927HVQQ/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5927HVQQ](/measurement-sets/IGVFDS5927HVQQ/) 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/IGVFDS5927HVQQ/"
}
]
},
"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": "2025-03-19T19:57:09.134340+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/IGVFDO7387JZDV/",
"accession": "IGVFDO7387JZDV",
"aliases": [
"igvf:corces_donor_BANN1349"
],
"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/IGVFDO7815RLQM/",
"accession": "IGVFDO7815RLQM",
"aliases": [
"igvf:corces_donor_BANN1504"
],
"sex": "female",
"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/IGVFDO2028IGVN/",
"accession": "IGVFDO2028IGVN",
"aliases": [
"igvf:corces_donor_BANN1256"
],
"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/IGVFDO4053HEKW/",
"accession": "IGVFDO4053HEKW",
"aliases": [
"igvf:corces_donor_BANN1317"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7942OOZA/",
"accession": "IGVFFI7942OOZA",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:16.647101+00:00",
"file_format": "fastq",
"file_size": 1428338829,
"href": "/sequence-files/IGVFFI7942OOZA/@@download/IGVFFI7942OOZA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/779fc6ad-2774-4071-b274-f60b9413e6b5/IGVFFI7942OOZA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1204NCRP/",
"accession": "IGVFFI1204NCRP",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:24.086599+00:00",
"file_format": "fastq",
"file_size": 3143563523,
"href": "/sequence-files/IGVFFI1204NCRP/@@download/IGVFFI1204NCRP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/d51dc4f0-5fc8-4658-9d8c-d1d35db9a160/IGVFFI1204NCRP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8700OUUX/",
"accession": "IGVFFI8700OUUX",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:20.324082+00:00",
"file_format": "fastq",
"file_size": 13018888268,
"href": "/sequence-files/IGVFFI8700OUUX/@@download/IGVFFI8700OUUX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/82d5302e-568c-4d5d-9082-3ca471daece4/IGVFFI8700OUUX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6746RQKD/",
"accession": "IGVFFI6746RQKD",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L005_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:30.549195+00:00",
"file_format": "fastq",
"file_size": 1416139432,
"href": "/sequence-files/IGVFFI6746RQKD/@@download/IGVFFI6746RQKD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/6aaaa4d6-c7ec-4c2f-b85a-8a1e443668c4/IGVFFI6746RQKD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2067XVHB/",
"accession": "IGVFFI2067XVHB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:40.891470+00:00",
"file_format": "fastq",
"file_size": 12494642839,
"href": "/sequence-files/IGVFFI2067XVHB/@@download/IGVFFI2067XVHB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/782c2e98-d8ce-4193-912c-9246ee015e32/IGVFFI2067XVHB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L005_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3601OLPT/",
"accession": "IGVFFI3601OLPT",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:27.084881+00:00",
"file_format": "fastq",
"file_size": 12446238292,
"href": "/sequence-files/IGVFFI3601OLPT/@@download/IGVFFI3601OLPT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/db13fa24-65ec-41b1-8630-15619b85bbe6/IGVFFI3601OLPT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1203RCNN/",
"accession": "IGVFFI1203RCNN",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:33.782649+00:00",
"file_format": "fastq",
"file_size": 13035169936,
"href": "/sequence-files/IGVFFI1203RCNN/@@download/IGVFFI1203RCNN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/fc252185-a4cb-48ac-9490-bb0f0210eeab/IGVFFI1203RCNN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6029OWVO/",
"accession": "IGVFFI6029OWVO",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G4_P075_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:00:37.783062+00:00",
"file_format": "fastq",
"file_size": 3137351340,
"href": "/sequence-files/IGVFFI6029OWVO/@@download/IGVFFI6029OWVO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/ef9e3f38-0218-4f11-85e6-0716d0665f71/IGVFFI6029OWVO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G4_L004_P075_S20_L005_R2_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/IGVFFI7587TJLC/"
],
"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/IGVFDS6570CCTQ/",
"accession": "IGVFDS6570CCTQ",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM1367EGUO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1367EGUO",
"aliases": [
"igvf:corces_multiplexedSample_RP026_G4"
],
"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": "2025-03-21T01:00:16.647101+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "da456b51-c906-4b8e-bbb4-c79425e8c9ac"
}