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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7070YJKH](/measurement-sets/IGVFDS7070YJKH/) has sequence file(s): [IGVFFI9247LGAI](/sequence-files/IGVFFI9247LGAI/), [IGVFFI1081IKUC](/sequence-files/IGVFFI1081IKUC/), [IGVFFI3526CVUL](/sequence-files/IGVFFI3526CVUL/), [IGVFFI4870YJFY](/sequence-files/IGVFFI4870YJFY/), [IGVFFI1343TLNG](/sequence-files/IGVFFI1343TLNG/), [IGVFFI6871EANY](/sequence-files/IGVFFI6871EANY/), [IGVFFI4367XQAW](/sequence-files/IGVFFI4367XQAW/), [IGVFFI8222WSTJ](/sequence-files/IGVFFI8222WSTJ/) 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/IGVFDS7070YJKH/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7070YJKH](/measurement-sets/IGVFDS7070YJKH/) 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/IGVFDS7070YJKH/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS7070YJKH](/measurement-sets/IGVFDS7070YJKH/) 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/IGVFDS7070YJKH/"
}
]
},
"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": "2025-03-19T19:57:17.783615+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7815RLQM/",
"accession": "IGVFDO7815RLQM",
"aliases": [
"igvf:corces_donor_BANN1504"
],
"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"
},
{
"@id": "/human-donors/IGVFDO9211DWXZ/",
"accession": "IGVFDO9211DWXZ",
"aliases": [
"igvf:corces_donor_BANN1352"
],
"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/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/IGVFFI9247LGAI/",
"accession": "IGVFFI9247LGAI",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:33.402638+00:00",
"file_format": "fastq",
"file_size": 14129959143,
"href": "/sequence-files/IGVFFI9247LGAI/@@download/IGVFFI9247LGAI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/73918496-2d59-47e9-a172-a606b751781d/IGVFFI9247LGAI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L005_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1081IKUC/",
"accession": "IGVFFI1081IKUC",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:20.258087+00:00",
"file_format": "fastq",
"file_size": 14015009373,
"href": "/sequence-files/IGVFFI1081IKUC/@@download/IGVFFI1081IKUC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/fe584258-aded-4da4-b674-f4f9acc69b54/IGVFFI1081IKUC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3526CVUL/",
"accession": "IGVFFI3526CVUL",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:16.370120+00:00",
"file_format": "fastq",
"file_size": 3544367298,
"href": "/sequence-files/IGVFFI3526CVUL/@@download/IGVFFI3526CVUL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/81d1f491-9c39-4179-a81b-12c0c79602eb/IGVFFI3526CVUL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4870YJFY/",
"accession": "IGVFFI4870YJFY",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:08.872717+00:00",
"file_format": "fastq",
"file_size": 1645036297,
"href": "/sequence-files/IGVFFI4870YJFY/@@download/IGVFFI4870YJFY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/f7e4a22f-b8fe-4729-b5ec-4092d9edbcad/IGVFFI4870YJFY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1343TLNG/",
"accession": "IGVFFI1343TLNG",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:13.242870+00:00",
"file_format": "fastq",
"file_size": 14582723627,
"href": "/sequence-files/IGVFFI1343TLNG/@@download/IGVFFI1343TLNG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/500b4826-f049-4ca6-b177-c7161701924f/IGVFFI1343TLNG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6871EANY/",
"accession": "IGVFFI6871EANY",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L005_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:23.836122+00:00",
"file_format": "fastq",
"file_size": 1641827804,
"href": "/sequence-files/IGVFFI6871EANY/@@download/IGVFFI6871EANY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/c4286800-f1df-4402-acfe-c8fa8247f320/IGVFFI6871EANY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4367XQAW/",
"accession": "IGVFFI4367XQAW",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:30.594868+00:00",
"file_format": "fastq",
"file_size": 3550573689,
"href": "/sequence-files/IGVFFI4367XQAW/@@download/IGVFFI4367XQAW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/db59d828-9a76-4495-8758-3e234382772d/IGVFFI4367XQAW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8222WSTJ/",
"accession": "IGVFFI8222WSTJ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP026_G8_P075_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:02:26.854372+00:00",
"file_format": "fastq",
"file_size": 14662630109,
"href": "/sequence-files/IGVFFI8222WSTJ/@@download/IGVFFI8222WSTJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/aba25980-1868-4fe9-846c-7689c36a35fd/IGVFFI8222WSTJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP026_G8_L008_P075_S24_L005_R1_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/IGVFDS9706KRLB/",
"accession": "IGVFDS9706KRLB",
"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": "2025-03-21T01:02:08.872717+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "fc23a1ab-9412-4fff-9199-e72e5dd72320"
}