{
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{
"category": "missing sequence specification",
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},
{
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{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS0865NCHS](/measurement-sets/IGVFDS0865NCHS/) 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/IGVFDS0865NCHS/"
}
]
},
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"@id": "/awards/HG012076/",
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"contact_pi": {
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"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"data_use_limitation_summaries": [
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],
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{
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],
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},
{
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"igvf:corces_donor_BANN1637"
],
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},
{
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],
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},
{
"@id": "/human-donors/IGVFDO7678VYKP/",
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],
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},
{
"@id": "/human-donors/IGVFDO1464XWYC/",
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"igvf:corces_donor_BANN1809"
],
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},
{
"@id": "/human-donors/IGVFDO5410JIJT/",
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"igvf:corces_donor_BANN0919"
],
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},
{
"@id": "/human-donors/IGVFDO7109IWDJ/",
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"igvf:corces_donor_BANN2005"
],
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"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0112XZXT/",
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"igvf:corces_donor_BANN0218"
],
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"status": "preview",
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}
],
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{
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],
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},
{
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],
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},
{
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],
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"href": "/sequence-files/IGVFFI6319RTZW/@@download/IGVFFI6319RTZW.fastq.gz",
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},
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},
{
"@id": "/sequence-files/IGVFFI3296ZPKW/",
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],
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"s3_uri": "s3://igvf-files/2025/03/21/02602f7b-a665-4e6e-a3cf-8c051ee36465/IGVFFI3296ZPKW.fastq.gz",
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9167QPVU/",
"accession": "IGVFFI9167QPVU",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP027_G4_P076_L005_R1"
],
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"s3_uri": "s3://igvf-files/2025/03/21/754e02b4-ff6c-4b2b-bfd1-6a8f1500322e/IGVFFI9167QPVU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "Multiome_RNA_RP027_G4_L004_P076_S52_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9427BHEE/",
"accession": "IGVFFI9427BHEE",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP027_G4_P076_L005_R2"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T00:18:03.391841+00:00",
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"file_size": 10910697757,
"href": "/sequence-files/IGVFFI9427BHEE/@@download/IGVFFI9427BHEE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/83239880-db8d-453c-8886-8eda00e43af2/IGVFFI9427BHEE.fastq.gz",
"sequencing_platform": {
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"term_name": "Illumina NovaSeq X"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7817HUJQ/",
"accession": "IGVFFI7817HUJQ",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP027_G4_P076_L006_I1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T00:18:06.984069+00:00",
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"file_size": 1280797693,
"href": "/sequence-files/IGVFFI7817HUJQ/@@download/IGVFFI7817HUJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/81ffc461-5c18-4ba0-aac8-c500a8b76de5/IGVFFI7817HUJQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "Multiome_RNA_RP027_G4_L004_P076_S52_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6895CIRR/",
"accession": "IGVFFI6895CIRR",
"aliases": [
"igvf:corces_sequenceFile_RNA_RP027_G4_P076_L006_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T00:18:10.235328+00:00",
"file_format": "fastq",
"file_size": 1044026610,
"href": "/sequence-files/IGVFFI6895CIRR/@@download/IGVFFI6895CIRR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/154f0500-31c6-4fc0-9386-8f9f24719819/IGVFFI6895CIRR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_RP027_G4_L004_P076_S52_L006_I2_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/IGVFDS9441JIJG/",
"accession": "IGVFDS9441JIJG",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM5603MWWM/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM5603MWWM",
"aliases": [
"igvf:corces_multiplexedSample_RP027_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"
}
],
"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 (male, 70 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment; Homo sapiens (male, 85 years) posterior cingulate 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": "2025-03-21T00:17:51.641752+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "709e63cc-d2b0-4dfb-bfcf-1ad2a6acfbe8"
}