{
"@context": "/terms/",
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"FileSet",
"Item"
],
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"aliases": [
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],
"assay_term": {
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"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2461OEPS](/measurement-sets/IGVFDS2461OEPS/) 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/IGVFDS2461OEPS/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS2461OEPS](/measurement-sets/IGVFDS2461OEPS/) 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/IGVFDS2461OEPS/"
}
]
},
"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": true,
"creation_timestamp": "2025-03-05T19:51:38.224000+00:00",
"data_use_limitation_summaries": [
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],
"donors": [
{
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"accession": "IGVFDO3350UAIM",
"aliases": [
"leif-ludwig:donor2304513004"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:17:29.676871+00:00",
"file_format": "yaml",
"file_size": 1504,
"href": "/configuration-files/IGVFFI3015GPXO/@@download/IGVFFI3015GPXO.yaml.gz",
"md5sum": "1b3b2f36233a8bd0e8703420edff5319",
"s3_uri": "s3://igvf-files/2025/03/18/ea8f5004-3690-43cb-b061-04d78ffea249/IGVFFI3015GPXO.yaml.gz",
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/projects/ludwig-igvf/IGVF/NEW_seqspecs/new_seqspecs_part1/seqspecs_samples_16-28/measurement2304513004_scATAC_L001.spec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2950PVUT/",
"accession": "IGVFFI2950PVUT",
"aliases": [
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],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-06T14:59:52.244357+00:00",
"file_format": "fastq",
"file_size": 6898764997,
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"md5sum": "e978aa5cb2825f08863c66d13e645042",
"s3_uri": "s3://igvf-restricted-files/2025/03/06/d31c62b9-21f2-4932-ba0a-9d301045c5f8/IGVFFI2950PVUT.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_2304513004_Y65F_mtMultiome_ATAC_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0537YEWI/",
"accession": "IGVFFI0537YEWI",
"aliases": [
"leif-ludwig:measurement2304513004_scATAC_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-06T14:54:45.267872+00:00",
"file_format": "fastq",
"file_size": 21448716269,
"href": "/sequence-files/IGVFFI0537YEWI/@@download/IGVFFI0537YEWI.fastq.gz",
"md5sum": "bd021c2c7f09eb058f2a654b95f79c8c",
"s3_uri": "s3://igvf-restricted-files/2025/03/06/763d84d3-89cb-4b0c-99da-10921bf93eb8/IGVFFI0537YEWI.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7445LCZH/",
"accession": "IGVFFI7445LCZH",
"aliases": [
"leif-ludwig:measurement2304513004_scATAC_R3"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-06T15:02:13.972593+00:00",
"file_format": "fastq",
"file_size": 20657902262,
"href": "/sequence-files/IGVFFI7445LCZH/@@download/IGVFFI7445LCZH.fastq.gz",
"md5sum": "20a4d27bbb75e9c49959796331b9ef09",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/scratch/groups/ludwig/Josch/IGVF_aging_fastq_final/SCT_2304513004_Y65F_mtMultiome_ATAC_S1_L001_R3_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/leif-ludwig/",
"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": [
"/tabular-files/IGVFFI7587TJLC/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome with scMito-seq",
"protocols": [
"https://www.protocols.io/view/mtscmultiome-atac-gex-protocol-d554888w"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS3673REVP/",
"accession": "IGVFDS3673REVP",
"status": "preview"
}
],
"samples": [
{
"@id": "/primary-cells/IGVFSM0371BTPA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0371BTPA",
"aliases": [
"leif-ludwig:sample2304513004"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/426307fa-9064-4824-a88a-2e033218fc6c/",
"certificate_identifier": "IP115-11",
"controlled_access": true,
"data_use_limitation": "GRU",
"data_use_limitation_modifiers": [
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],
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_2000001/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "peripheral blood mononuclear cell",
"term_name": "peripheral blood mononuclear cell"
}
],
"status": "preview",
"summary": "Homo sapiens (female, 65 years) peripheral blood mononuclear cell",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
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"title": "Ludwig Lab"
},
"submitted_files_timestamp": "2025-03-06T14:54:45.267872+00:00",
"summary": "10x multiome with scMito-seq",
"uuid": "9c18b626-6244-4b59-aab8-2db39b09d990"
}