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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0577OKVB](/measurement-sets/IGVFDS0577OKVB/) has sequence file(s): [IGVFFI6198TQUQ](/sequence-files/IGVFFI6198TQUQ/), [IGVFFI8344ZNWJ](/sequence-files/IGVFFI8344ZNWJ/), [IGVFFI3422FXRS](/sequence-files/IGVFFI3422FXRS/), [IGVFFI6605YIPR](/sequence-files/IGVFFI6605YIPR/), [IGVFFI6346BBHV](/sequence-files/IGVFFI6346BBHV/), [IGVFFI1587MCOD](/sequence-files/IGVFFI1587MCOD/), [IGVFFI1311NBED](/sequence-files/IGVFFI1311NBED/), [IGVFFI1678PHBK](/sequence-files/IGVFFI1678PHBK/) 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/IGVFDS0577OKVB/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0577OKVB](/measurement-sets/IGVFDS0577OKVB/) 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/IGVFDS0577OKVB/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS0577OKVB](/measurement-sets/IGVFDS0577OKVB/) 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/IGVFDS0577OKVB/"
}
]
},
"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": "2025-03-19T19:57:00.294129+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO5718REZU/",
"accession": "IGVFDO5718REZU",
"aliases": [
"igvf:corces_donor_BANN9926"
],
"sex": "female",
"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/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/IGVFDO9211DWXZ/",
"accession": "IGVFDO9211DWXZ",
"aliases": [
"igvf:corces_donor_BANN1352"
],
"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/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/IGVFFI6198TQUQ/",
"accession": "IGVFFI6198TQUQ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L005_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:59:05.218276+00:00",
"file_format": "fastq",
"file_size": 1336959191,
"href": "/sequence-files/IGVFFI6198TQUQ/@@download/IGVFFI6198TQUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/098d27c8-6d7a-4cc0-9b1f-6521de3cc3a4/IGVFFI6198TQUQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8344ZNWJ/",
"accession": "IGVFFI8344ZNWJ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:58:47.406628+00:00",
"file_format": "fastq",
"file_size": 1344628229,
"href": "/sequence-files/IGVFFI8344ZNWJ/@@download/IGVFFI8344ZNWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/9626bc2f-f0f6-4a38-8101-09e682f6f283/IGVFFI8344ZNWJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3422FXRS/",
"accession": "IGVFFI3422FXRS",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:58:52.255238+00:00",
"file_format": "fastq",
"file_size": 12432673192,
"href": "/sequence-files/IGVFFI3422FXRS/@@download/IGVFFI3422FXRS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/2ea824be-a548-4f74-93c6-5103d4994faf/IGVFFI3422FXRS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6605YIPR/",
"accession": "IGVFFI6605YIPR",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:58:55.900531+00:00",
"file_format": "fastq",
"file_size": 3013507661,
"href": "/sequence-files/IGVFFI6605YIPR/@@download/IGVFFI6605YIPR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/cfaadf3b-e305-4f97-b185-ea10e7f7388b/IGVFFI6605YIPR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6346BBHV/",
"accession": "IGVFFI6346BBHV",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:59:01.174626+00:00",
"file_format": "fastq",
"file_size": 11949496540,
"href": "/sequence-files/IGVFFI6346BBHV/@@download/IGVFFI6346BBHV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/7fdc3159-6c84-4753-8dea-b3a3c1bf93a5/IGVFFI6346BBHV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1587MCOD/",
"accession": "IGVFFI1587MCOD",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:59:09.139531+00:00",
"file_format": "fastq",
"file_size": 12501873474,
"href": "/sequence-files/IGVFFI1587MCOD/@@download/IGVFFI1587MCOD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/ddba42a0-875e-4751-91bd-e8a3ec931dac/IGVFFI1587MCOD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1311NBED/",
"accession": "IGVFFI1311NBED",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:59:12.640489+00:00",
"file_format": "fastq",
"file_size": 3018492779,
"href": "/sequence-files/IGVFFI1311NBED/@@download/IGVFFI1311NBED.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/85812a45-dee5-4fb4-8c6c-b8f6743e691d/IGVFFI1311NBED.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1678PHBK/",
"accession": "IGVFFI1678PHBK",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G1_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:59:16.340895+00:00",
"file_format": "fastq",
"file_size": 12041561316,
"href": "/sequence-files/IGVFFI1678PHBK/@@download/IGVFFI1678PHBK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/6cfc905e-0ad4-451c-994a-4cab9f3ab5f1/IGVFFI1678PHBK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G1_L001_P075_S17_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/IGVFDS0821GFDR/",
"accession": "IGVFDS0821GFDR",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM0921NWYJ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM0921NWYJ",
"aliases": [
"igvf:corces_multiplexedSample_RP026_G1"
],
"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": "2025-03-21T00:58:47.406628+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "91781efa-c7ab-45e2-8b00-8bed5c3e535f"
}