GSE280401

GSE280401 is the Gene Expression Omnibus accession for the PBMC single-cell RNA-seq data generated by Tkachenko et al. 2024 for type 2 diabetes transcriptomic analysis.

Dataset Facts

• scRNA-seq was performed on PBMCs isolated from 2 T2D patients and 2 healthy controls.
• All 4 subjects were female, with no family history of T2D.
• After quality filtering, 6,974 cells remained for analysis.
• 10x Genomics Chromium platform, 3’ single-cell chemistry (v3.1), sequenced on Illumina HiSeq 2500 as 75 bp PE reads.
• Data processed with CellRanger v8.0.0, analyzed with Seurat v5.1.0.
• Subjects 2 and 4 (T2D subject and one healthy control) were also included in the GSE280402 bulk RNA-seq experiment.

Paper-Relevant Use

• GSE280401 provides a small-scale PBMC scRNA-seq dataset from a Russian cohort, complementing larger studies like GSE268210 (Gu et al. 2024, Korean cohort).
• The dataset shows NK cell depletion in T2D PBMCs and increased CD4+ TCM/naive cells, contrasting with Gu et al. 2024.
• Sample size (n=2/group) limits statistical power; findings should be treated as preliminary.

Links

• Tkachenko et al. 2024
• GSE280402 — companion bulk RNA-seq accession from the same study
• PBMC Immune Changes in Type 2 Diabetes
• Type 2 Diabetes PBMC Ancestry Paper