{
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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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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1757WXOT](/measurement-sets/IGVFDS1757WXOT/) has sequence file(s): [IGVFFI9781UMKW](/sequence-files/IGVFFI9781UMKW/), [IGVFFI0292SWAQ](/sequence-files/IGVFFI0292SWAQ/), [IGVFFI8194MWAS](/sequence-files/IGVFFI8194MWAS/), [IGVFFI1536KNLF](/sequence-files/IGVFFI1536KNLF/), [IGVFFI3777WNAN](/sequence-files/IGVFFI3777WNAN/), [IGVFFI4513RZCG](/sequence-files/IGVFFI4513RZCG/), [IGVFFI8080PPHB](/sequence-files/IGVFFI8080PPHB/), [IGVFFI4399PLFX](/sequence-files/IGVFFI4399PLFX/) 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.",
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},
{
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{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS1757WXOT](/measurement-sets/IGVFDS1757WXOT/) 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/IGVFDS1757WXOT/"
}
]
},
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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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],
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},
{
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"igvf:corces_donor_BANN0526"
],
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},
{
"@id": "/human-donors/IGVFDO1464XWYC/",
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],
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},
{
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"igvf:corces_donor_BANN1235"
],
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},
{
"@id": "/human-donors/IGVFDO7109IWDJ/",
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"igvf:corces_donor_BANN2005"
],
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},
{
"@id": "/human-donors/IGVFDO0180JQCL/",
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"igvf:corces_donor_BANN1344"
],
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},
{
"@id": "/human-donors/IGVFDO5410JIJT/",
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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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},
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},
{
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"accession": "IGVFFI1536KNLF",
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],
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},
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},
{
"@id": "/sequence-files/IGVFFI3777WNAN/",
"accession": "IGVFFI3777WNAN",
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"igvf:corces_sequenceFile_ATAC_RP027_G5_P075_L005_R2"
],
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"s3_uri": "s3://igvf-files/2025/03/21/797bf716-497a-47e5-af5c-af2683ad5249/IGVFFI3777WNAN.fastq.gz",
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"status": "released",
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},
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"submitted_file_name": "Multiome_ATAC_RP027_G5_L005_P075_S29_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4513RZCG/",
"accession": "IGVFFI4513RZCG",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G5_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:35.232062+00:00",
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"href": "/sequence-files/IGVFFI4513RZCG/@@download/IGVFFI4513RZCG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/78defa7f-67e4-4a50-ad02-60f7b259c538/IGVFFI4513RZCG.fastq.gz",
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8080PPHB/",
"accession": "IGVFFI8080PPHB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G5_P075_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:21.343407+00:00",
"file_format": "fastq",
"file_size": 3270893551,
"href": "/sequence-files/IGVFFI8080PPHB/@@download/IGVFFI8080PPHB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/83d89f91-adb1-44ee-8fca-019fe9bb2414/IGVFFI8080PPHB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "Multiome_ATAC_RP027_G5_L005_P075_S29_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4399PLFX/",
"accession": "IGVFFI4399PLFX",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G5_P075_L005_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:29.863943+00:00",
"file_format": "fastq",
"file_size": 13480038035,
"href": "/sequence-files/IGVFFI4399PLFX/@@download/IGVFFI4399PLFX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/c0bb320f-b8d1-4540-86d5-475ac3da445f/IGVFFI4399PLFX.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G5_L005_P075_S29_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/IGVFDS3899HTRC/",
"accession": "IGVFDS3899HTRC",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7865MTXP/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7865MTXP",
"aliases": [
"igvf:corces_multiplexedSample_RP027_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"
}
],
"institutional_certificates": [
{
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"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": "2025-03-21T01:04:16.473409+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "e1e60fea-12b0-4bb0-bb90-9782cfe1858f"
}