{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
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],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
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"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4930QMXA](/measurement-sets/IGVFDS4930QMXA/) 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/IGVFDS4930QMXA/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS4930QMXA](/measurement-sets/IGVFDS4930QMXA/) 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/IGVFDS4930QMXA/"
}
]
},
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"component": "mapping",
"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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"creation_timestamp": "2025-03-05T19:51:22.324103+00:00",
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{
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],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"aliases": [
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],
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"file_format": "yaml",
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"status": "preview",
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"upload_status": "validated"
},
{
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],
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},
{
"@id": "/sequence-files/IGVFFI7783ANIV/",
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],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-06T11:28:14.694715+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7783ANIV/@@download/IGVFFI7783ANIV.fastq.gz",
"s3_uri": "s3://igvf-restricted-files/2025/03/06/c02d2999-9525-4c60-87b4-6aaf6bb1e86c/IGVFFI7783ANIV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
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"submitted_file_name": "/data/cephfs-1/scratch/groups/ludwig/Josch/IGVF_aging_fastq_final/SCT_2304404009_Y29M_mtMultiome_ATAC_S1_L001_R3_001.fastq.gz",
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},
{
"@id": "/sequence-files/IGVFFI1818SNUW/",
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"creation_timestamp": "2025-03-06T11:05:38.604628+00:00",
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"sequencing_platform": {
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"status": "released",
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"upload_status": "validated"
}
],
"input_for": [],
"lab": {
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"title": "Leif Ludwig, MDC"
},
"multiome_size": 2,
"notes": "This measurement set previously used scMito-seq as a preferred_assay_title, but this enum is now replaced with 10x multiome with scMito-seq.",
"onlist_files": [
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],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome with scMito-seq",
"protocols": [
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],
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{
"@id": "/measurement-sets/IGVFDS8153TZWE/",
"accession": "IGVFDS8153TZWE",
"status": "preview"
}
],
"samples": [
{
"@id": "/primary-cells/IGVFSM2747IYLG/",
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"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2747IYLG",
"aliases": [
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],
"classifications": [
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],
"institutional_certificates": [
{
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"controlled_access": true,
"data_use_limitation": "GRU",
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"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_2000001/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "peripheral blood mononuclear cell",
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}
],
"status": "preview",
"summary": "Homo sapiens (male, 29 years) peripheral blood mononuclear cell",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
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"submitted_by": {
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"title": "Ludwig Lab"
},
"submitted_files_timestamp": "2025-03-06T11:05:38.604628+00:00",
"summary": "10x multiome with scMito-seq",
"uuid": "608e9dbf-9f10-4310-9a37-7b3aa2b6179f"
}