RIDA_v1.0 — Russian Immune Diversity Atlas
The Russian Immune Diversity Atlas (RIDA_v1.0) is the primary dataset for this paper. It is a multi-site PBMC biobank collected to study immune diversity and type 2 diabetes ancestry-associated immune differences across the Russian Federation.
Collection Sites
| Site | City | Region |
|---|---|---|
| Moscow | Moscow | Central Russia |
| Kazan | Kazan | Volga Region (Tatarstan) |
| Grozny | Grozny | North Caucasus (Chechnya) |
| Yakutsk | Yakutsk | Far East (Sakha/Yakutia) |
RIDA_v2.0 extends the atlas with an additional site in Ufa (Bashkortostan) but is outside the scope of this paper.
Scope
- v1.0 (this paper): 4 sites — Moscow, Kazan, Grozny, Yakutsk
- v2.0: adds Ufa — out of scope for the current paper
Data Types (per paper scope)
- PBMC isolation and cryopreservation
- Genotyping data (ancestry separation via ADMIXTURE)
- Single-cell PBMC profiling (scRNA-seq / scATAC-seq)
- Immune profiling (flow cytometry, functional assays)
- Clinical metadata (T2D status, anthropometrics, biochemistry panels)
Related Pages
- Methods — Manuscript Draft
- PBMC Isolation Protocol
- Markelova et al. 2025
- Type 2 Diabetes PBMC Ancestry Paper
Software and Algorithms
Key software used in the study:
- DRAGEN Single-Cell RNA pipeline v3.8.4
- Cell Ranger v7.0.1 (10x Genomics)
- Demuxlet (Kang et al.)
- Seurat v4.1.1 (Hao et al.)
- RCAv2 (Schmidt et al.)
- DoubletFinder v2.0.3 (McGinnis et al.)
- scanpy v1.11.4 (Wolf et al.)
- pertpy v1.0.1 (Heumos et al.)
- GenomeStudio v2.0 (Illumina)
- PLINK 2.0 (Chang et al.)
- bcftools (Danecek et al.)
- pySCENIC v0.12.0
- Monocle3, tradeSeq, ComplexHeatmap, clusterProfiler
- decoupler, msigdbr, OmniPath
Key Reagents and Assays
| Reagent/Kit | Supplier | Catalog |
|---|---|---|
| Library Construction Kit, 16 rxns | 10x Genomics | PN-1000190 |
| QIAamp DNA Mini Kit | Qiagen | 51306 |
| Illumina GSAv3.0 array | Illumina | 20030770 |
| Chromium Controller | 10x Genomics | PN-120270 |
Data Deposition
- Gene-cell matrices and metadata: Available by data access application to the corresponding authors
- Deidentified FASTQ files: Available by data access application to the corresponding authors