{
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{
"category": "missing sequence specification",
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{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS8780GGCL](/measurement-sets/IGVFDS8780GGCL/) 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/IGVFDS8780GGCL/"
}
]
},
"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"
},
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"controlled_access": false,
"creation_timestamp": "2025-03-19T19:57:22.330658+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
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{
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"igvf:corces_donor_BANN1235"
],
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},
{
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"igvf:corces_donor_BANN2005"
],
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},
{
"@id": "/human-donors/IGVFDO9028PIDF/",
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"igvf:corces_donor_BANN1637"
],
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},
{
"@id": "/human-donors/IGVFDO5410JIJT/",
"accession": "IGVFDO5410JIJT",
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"igvf:corces_donor_BANN0919"
],
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"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0112XZXT/",
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"igvf:corces_donor_BANN0218"
],
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},
{
"@id": "/human-donors/IGVFDO1464XWYC/",
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"igvf:corces_donor_BANN1809"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0180JQCL/",
"accession": "IGVFDO0180JQCL",
"aliases": [
"igvf:corces_donor_BANN1344"
],
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"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4015EJFT/",
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"igvf:corces_donor_BANN0526"
],
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"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"accession": "IGVFFI9326ACRY",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L004_I1"
],
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"href": "/sequence-files/IGVFFI9326ACRY/@@download/IGVFFI9326ACRY.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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},
{
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],
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"status": "released",
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI6891JGGP",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L004_R2"
],
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"creation_timestamp": "2025-03-21T01:03:11.009566+00:00",
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"href": "/sequence-files/IGVFFI6891JGGP/@@download/IGVFFI6891JGGP.fastq.gz",
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5871POWQ/",
"accession": "IGVFFI5871POWQ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L004_R3"
],
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"href": "/sequence-files/IGVFFI5871POWQ/@@download/IGVFFI5871POWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/69717f84-a854-4caa-b193-b060fccb2674/IGVFFI5871POWQ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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},
{
"@id": "/sequence-files/IGVFFI3388KLUV/",
"accession": "IGVFFI3388KLUV",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L005_R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T01:03:19.916045+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI3388KLUV/@@download/IGVFFI3388KLUV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/359d5e8f-cf25-46ae-a0b0-41156961bdb8/IGVFFI3388KLUV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G2_L002_P075_S26_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3420BQFP/",
"accession": "IGVFFI3420BQFP",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L005_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:03:17.040357+00:00",
"file_format": "fastq",
"file_size": 1662872992,
"href": "/sequence-files/IGVFFI3420BQFP/@@download/IGVFFI3420BQFP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/029f74bb-dbab-4f3c-bd7f-9bd6a9ae80d6/IGVFFI3420BQFP.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "Multiome_ATAC_RP027_G2_L002_P075_S26_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6665FWVS/",
"accession": "IGVFFI6665FWVS",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:03:23.548597+00:00",
"file_format": "fastq",
"file_size": 3769300847,
"href": "/sequence-files/IGVFFI6665FWVS/@@download/IGVFFI6665FWVS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/f492e87b-508a-4aba-82d2-6439889e9eee/IGVFFI6665FWVS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G2_L002_P075_S26_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2601GLRW/",
"accession": "IGVFFI2601GLRW",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G2_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:03:28.322421+00:00",
"file_format": "fastq",
"file_size": 15013117469,
"href": "/sequence-files/IGVFFI2601GLRW/@@download/IGVFFI2601GLRW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/5db72a96-2be9-4a15-b1ed-cb449522de02/IGVFFI2601GLRW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G2_L002_P075_S26_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/IGVFDS7811WDIP/",
"accession": "IGVFDS7811WDIP",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9924QRZP/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9924QRZP",
"aliases": [
"igvf:corces_multiplexedSample_RP027_G2"
],
"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": "2025-03-21T01:03:05.227061+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "12385164-9dc0-44e9-9ea4-a107f15ad2b3"
}