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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5084HGGY](/measurement-sets/IGVFDS5084HGGY/) has sequence file(s): [IGVFFI6593RZAC](/sequence-files/IGVFFI6593RZAC/), [IGVFFI6741EFPA](/sequence-files/IGVFFI6741EFPA/), [IGVFFI8136QRBL](/sequence-files/IGVFFI8136QRBL/), [IGVFFI7771XOKD](/sequence-files/IGVFFI7771XOKD/), [IGVFFI7689STLO](/sequence-files/IGVFFI7689STLO/), [IGVFFI6952YKRW](/sequence-files/IGVFFI6952YKRW/), [IGVFFI0937JWCK](/sequence-files/IGVFFI0937JWCK/), [IGVFFI2823FLXO](/sequence-files/IGVFFI2823FLXO/) 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/IGVFDS5084HGGY/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5084HGGY](/measurement-sets/IGVFDS5084HGGY/) 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/IGVFDS5084HGGY/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5084HGGY](/measurement-sets/IGVFDS5084HGGY/) 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/IGVFDS5084HGGY/"
}
]
},
"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": "2025-03-19T21:45:04.715989+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": [
{
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"accession": "IGVFFI6593RZAC",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L005_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:29.392015+00:00",
"file_format": "fastq",
"file_size": 1271446754,
"href": "/sequence-files/IGVFFI6593RZAC/@@download/IGVFFI6593RZAC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/d07cd2fd-c091-4a53-82d9-448f218622d4/IGVFFI6593RZAC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6741EFPA/",
"accession": "IGVFFI6741EFPA",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L005_I1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:25.579776+00:00",
"file_format": "fastq",
"file_size": 1286033794,
"href": "/sequence-files/IGVFFI6741EFPA/@@download/IGVFFI6741EFPA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/56419702-2bb5-41e5-a343-21a26e453425/IGVFFI6741EFPA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8136QRBL/",
"accession": "IGVFFI8136QRBL",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L006_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:43.687639+00:00",
"file_format": "fastq",
"file_size": 1312535562,
"href": "/sequence-files/IGVFFI8136QRBL/@@download/IGVFFI8136QRBL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/6b1ecc94-5617-433f-80e3-068b64eaef3b/IGVFFI8136QRBL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7771XOKD/",
"accession": "IGVFFI7771XOKD",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L006_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:47.080370+00:00",
"file_format": "fastq",
"file_size": 18200459887,
"href": "/sequence-files/IGVFFI7771XOKD/@@download/IGVFFI7771XOKD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/8e3884f2-f11a-4c96-b9e8-f1531eb56650/IGVFFI7771XOKD.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7689STLO/",
"accession": "IGVFFI7689STLO",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:32.185150+00:00",
"file_format": "fastq",
"file_size": 17529032784,
"href": "/sequence-files/IGVFFI7689STLO/@@download/IGVFFI7689STLO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/b4377303-50d4-4656-a4a6-6796df8d4a72/IGVFFI7689STLO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6952YKRW/",
"accession": "IGVFFI6952YKRW",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L005_R2"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:35.894735+00:00",
"file_format": "fastq",
"file_size": 13142838924,
"href": "/sequence-files/IGVFFI6952YKRW/@@download/IGVFFI6952YKRW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/ff4e1b51-b486-4c84-bf56-2b832fc33963/IGVFFI6952YKRW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0937JWCK/",
"accession": "IGVFFI0937JWCK",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L006_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:39.619980+00:00",
"file_format": "fastq",
"file_size": 1338779947,
"href": "/sequence-files/IGVFFI0937JWCK/@@download/IGVFFI0937JWCK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/fd8d1ad1-33cd-4b0d-a6ec-14a7c2756461/IGVFFI0937JWCK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2823FLXO/",
"accession": "IGVFFI2823FLXO",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP026_G5_P076_L006_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:14:50.419187+00:00",
"file_format": "fastq",
"file_size": 13721286659,
"href": "/sequence-files/IGVFFI2823FLXO/@@download/IGVFFI2823FLXO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/81a77767-5b7a-4516-b299-fc7796972d71/IGVFFI2823FLXO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP026_G5_L005_P076_S45_L006_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/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/IGVFDS8256XMDW/",
"accession": "IGVFDS8256XMDW",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9967FNUH/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9967FNUH",
"aliases": [
"igvf:corces_multiplexedSample_RP026_G5"
],
"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": "2025-03-21T00:14:25.579776+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "285a794f-1495-4d1f-a2a5-7dfd9fec3e7b"
}