scRNA-seq of thymic epithelial cells from Aire-knockout rats

This dataset investigates the impact of Aire deficiency on thymic stromal cell subpopulations in rats using single-cell RNA sequencing (scRNA-seq). CD45-, EpCAM+ thymic epithelial cells (TECs) were isolated from the thymi of 6-week-old Aire-knockout (n=4) and Aire-heterozygous control (n=3) rats via flow cytometry. The cells underwent enzymatic digestion to enrich the stromal compartment, and single cells were processed using the 10x Chromium platform with barcoded cDNA libraries prepared using the single-cell 3’ mRNA kit. Sequencing was performed on the Illumina MiSeq platform, and gene expression data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) using Cell Ranger (v6.0.1). The dataset includes processed count matrices generated by Cell Ranger.

Methods
Thymi from 6-week-old Aire-knockout and Aire-heterozygous control rats were minced and gravity-sedimented to isolate stromal cells and thymocytes. Stromal cells were enriched through enzymatic digestion using collagenase, DNase, and dispase, and sorted into the CD45-, EpCAM+ population using flow cytometry. Single cells were captured with the 10x Chromium microfluidics system, and barcoded cDNA libraries were prepared using the 10x Genomics single-cell 3’ mRNA kit. Libraries were sequenced on the Illumina MiSeq platform, and the data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) and quantified using the Cell Ranger software suite (v6.0.1).