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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6846AEHO](/measurement-sets/IGVFDS6846AEHO/) has sequence file(s): [IGVFFI4761EILZ](/sequence-files/IGVFFI4761EILZ/), [IGVFFI6729LWFC](/sequence-files/IGVFFI6729LWFC/), [IGVFFI1508QBWJ](/sequence-files/IGVFFI1508QBWJ/), [IGVFFI6697SFYT](/sequence-files/IGVFFI6697SFYT/), [IGVFFI4548ZOPC](/sequence-files/IGVFFI4548ZOPC/), [IGVFFI4702OEGL](/sequence-files/IGVFFI4702OEGL/), [IGVFFI5958YYSM](/sequence-files/IGVFFI5958YYSM/), [IGVFFI2044WRQE](/sequence-files/IGVFFI2044WRQE/) 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/IGVFDS6846AEHO/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6846AEHO](/measurement-sets/IGVFDS6846AEHO/) 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/IGVFDS6846AEHO/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS6846AEHO](/measurement-sets/IGVFDS6846AEHO/) 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/IGVFDS6846AEHO/"
}
]
},
"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": "2025-03-19T19:57:13.095746+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
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"accession": "IGVFDO4053HEKW",
"aliases": [
"igvf:corces_donor_BANN1317"
],
"sex": "male",
"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/IGVFDO7815RLQM/",
"accession": "IGVFDO7815RLQM",
"aliases": [
"igvf:corces_donor_BANN1504"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@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/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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4761EILZ/",
"accession": "IGVFFI4761EILZ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:29.732820+00:00",
"file_format": "fastq",
"file_size": 14372309511,
"href": "/sequence-files/IGVFFI4761EILZ/@@download/IGVFFI4761EILZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/baf49c1f-728b-4f39-a406-2a86f591a54d/IGVFFI4761EILZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6729LWFC/",
"accession": "IGVFFI6729LWFC",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:15.573814+00:00",
"file_format": "fastq",
"file_size": 14312849273,
"href": "/sequence-files/IGVFFI6729LWFC/@@download/IGVFFI6729LWFC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/4656eb88-93c2-484d-87d8-0eb93906ddaf/IGVFFI6729LWFC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1508QBWJ/",
"accession": "IGVFFI1508QBWJ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:12.639115+00:00",
"file_format": "fastq",
"file_size": 1540410785,
"href": "/sequence-files/IGVFFI1508QBWJ/@@download/IGVFFI1508QBWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/557b2b1c-e5c5-40f5-af6d-185756857ce1/IGVFFI1508QBWJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6697SFYT/",
"accession": "IGVFFI6697SFYT",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:23.121214+00:00",
"file_format": "fastq",
"file_size": 13662644593,
"href": "/sequence-files/IGVFFI6697SFYT/@@download/IGVFFI6697SFYT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/75b120b7-417c-430d-8293-5b5db1a936ac/IGVFFI6697SFYT.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4548ZOPC/",
"accession": "IGVFFI4548ZOPC",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:19.696541+00:00",
"file_format": "fastq",
"file_size": 3453821114,
"href": "/sequence-files/IGVFFI4548ZOPC/@@download/IGVFFI4548ZOPC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/b815511a-7aa2-49ca-9ba8-a472b6f2b532/IGVFFI4548ZOPC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4702OEGL/",
"accession": "IGVFFI4702OEGL",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:33.360281+00:00",
"file_format": "fastq",
"file_size": 3455749001,
"href": "/sequence-files/IGVFFI4702OEGL/@@download/IGVFFI4702OEGL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/c7d768e4-a0e2-4da5-be07-cdc23a10b9dd/IGVFFI4702OEGL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5958YYSM/",
"accession": "IGVFFI5958YYSM",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L005_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:26.205876+00:00",
"file_format": "fastq",
"file_size": 1532838905,
"href": "/sequence-files/IGVFFI5958YYSM/@@download/IGVFFI5958YYSM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/ba3bfbdf-a7ac-4f05-a228-6ebbc065b4e4/IGVFFI5958YYSM.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2044WRQE/",
"accession": "IGVFFI2044WRQE",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G6_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:01:36.554300+00:00",
"file_format": "fastq",
"file_size": 13756073519,
"href": "/sequence-files/IGVFFI2044WRQE/@@download/IGVFFI2044WRQE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/0b7055ab-5f93-40df-b8f7-9ea8b65520be/IGVFFI2044WRQE.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G6_L006_P075_S22_L005_R3_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/IGVFDS1905QFFH/",
"accession": "IGVFDS1905QFFH",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM5241MOXO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM5241MOXO",
"aliases": [
"igvf:corces_multiplexedSample_RP026_G6"
],
"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": "2025-03-21T01:01:12.639115+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "de89c36f-070d-4eac-8531-087f51c00845"
}