scRNA-seq of splenic CD45+ Cells from Aire-knockout rats

This dataset examines the impact of anti-IFNα autoantibodies on immune cell populations and gene expression in peripheral immune tissues of Aire-knockout rats. Single-cell RNA sequencing (scRNA-seq) was performed on CD45+ splenic cells from 7-month-old Aire-knockout rats (n=4) with high levels of anti-IFNα autoantibodies and age-matched Aire-heterozygous controls (n=4). Splenic cells were isolated through mechanical homogenization, followed by erythrocyte lysis and CD45+ cell sorting using a MA900 cell sorter. Single cells were captured with the 10x Chromium microfluidics system, and barcoded cDNA libraries were prepared using the single-cell 3’ mRNA kit (10x Genomics). Sequencing was conducted 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. The dataset includes count matrices generated by Cell Ranger.

Methods
CD45+ splenic cells were isolated from 7-month-old Aire-knockout rats (n=4) with high levels of anti-IFNα autoantibodies and age-matched Aire-heterozygous controls (n=4). Spleens were homogenized mechanically, and erythrocytes were removed using an ACK lysis solution. The CD45+ cell population was sorted using a MA900 cell sorter (Sony Biotechnology). Single-cell RNA sequencing (scRNA-seq) was performed with the 10x Chromium microfluidics system, and barcoded cDNA libraries were constructed using the single-cell 3’ mRNA kit (10x Genomics). Sequencing was conducted on the Illumina MiSeq platform. The data were processed using the Cell Ranger software suite (Version 6.0.1, 10x Genomics Inc.) and aligned to the Rattus norvegicus reference genome (Rnor_6.0).