scRNA-seq of CD45+ cells from salivary gland of 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+ cells sorted from the submandibular salivary glands of seven-month-old Aire-deficient rats (n=4) and age-matched Aire-heterozygous control rats (n=3). The salivary glands were minced, enzymatically digested, and processed to avoid cell aggregation before sorting for CD45+ cells. The single cells were captured using the 10x Chromium platform, with cDNA libraries prepared using the single-cell 3’ mRNA kit. Sequencing was conducted on the Illumina MiSeq platform, and the data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) and processed with the Cell Ranger software suite. The dataset includes count matrices generated by Cell Ranger.

Methods
This dataset was collected by isolating CD45+ immune cells from the submandibular salivary glands of seven-month-old Aire-deficient rats (n=4) and age-matched Aire-heterozygous control rats (n=3). The salivary glands were minced and enzymatically digested using a combination of collagenase 4, DNase1, and Dispase to generate a single-cell suspension. The samples were processed to prevent aggregation and then sorted for CD45+ cells using an MA900 cell sorter. Single cells were captured using the 10x Chromium microfluidics platform, and barcoded cDNA libraries were prepared using the 10x Genomics single-cell 3’ mRNA kit. Sequencing was performed on the Illumina MiSeq platform, and the data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) using the Cell Ranger software suite.