{
"@context": "/terms/",
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"@type": [
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"FileSet",
"Item"
],
"accession": "IGVFDS0287IEKR",
"aliases": [
"leif-ludwig:measurement2306520006_scRNA"
],
"assay_term": {
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"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0287IEKR](/measurement-sets/IGVFDS0287IEKR/) 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/IGVFDS0287IEKR/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS0287IEKR](/measurement-sets/IGVFDS0287IEKR/) 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/IGVFDS0287IEKR/"
}
]
},
"award": {
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"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": "2025-03-05T19:51:28.528701+00:00",
"data_use_limitation_summaries": [
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],
"donors": [
{
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"accession": "IGVFDO8949AILT",
"aliases": [
"leif-ludwig:donor2306520006"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI7670ZJLA",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:16:10.732313+00:00",
"file_format": "yaml",
"file_size": 1469,
"href": "/configuration-files/IGVFFI7670ZJLA/@@download/IGVFFI7670ZJLA.yaml.gz",
"md5sum": "f5a91b7634f0111f9d6b978c9c021b79",
"s3_uri": "s3://igvf-files/2025/03/18/2f50a309-cfed-44dc-b13f-5128649d23b1/IGVFFI7670ZJLA.yaml.gz",
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/projects/ludwig-igvf/IGVF/NEW_seqspecs/new_seqspecs_part1/seqspecs_samples_16-28/measurement2306520006_scRNA_L001.spec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2020FEQU/",
"accession": "IGVFFI2020FEQU",
"aliases": [
"leif-ludwig:measurement2306520006_scRNA_R1"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-06T13:10:08.087322+00:00",
"file_format": "fastq",
"file_size": 7242524819,
"href": "/sequence-files/IGVFFI2020FEQU/@@download/IGVFFI2020FEQU.fastq.gz",
"md5sum": "927dc70f22cb9a5b1bc3fc1181248918",
"s3_uri": "s3://igvf-restricted-files/2025/03/06/d95fb347-ae75-45f3-8ca0-b63f7507dd8b/IGVFFI2020FEQU.fastq.gz",
"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_2306520006_Y70F_mtMultiome_GEX_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8771IDCN/",
"accession": "IGVFFI8771IDCN",
"aliases": [
"leif-ludwig:measurement2306520006_scRNA_R2"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-06T13:12:23.738360+00:00",
"file_format": "fastq",
"file_size": 15090941014,
"href": "/sequence-files/IGVFFI8771IDCN/@@download/IGVFFI8771IDCN.fastq.gz",
"md5sum": "6cce4823e85096c35fbd2ab377cd313f",
"s3_uri": "s3://igvf-restricted-files/2025/03/06/0ae678a0-deee-4394-b50d-5e0b818b2d88/IGVFFI8771IDCN.fastq.gz",
"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_2306520006_Y70F_mtMultiome_GEX_S1_L001_R2_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/IGVFFI8751YQRY/"
],
"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/IGVFDS2406JVCK/",
"accession": "IGVFDS2406JVCK",
"status": "preview"
}
],
"samples": [
{
"@id": "/primary-cells/IGVFSM1705OPIJ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1705OPIJ",
"aliases": [
"leif-ludwig:sample2306520006"
],
"classifications": [
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],
"institutional_certificates": [
{
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"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, 70 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": "2025-03-06T13:10:08.087322+00:00",
"summary": "10x multiome with scMito-seq",
"uuid": "0c43a1e2-5906-46a5-b30b-c1571eb7918d"
}