Transcriptome Profiling of CD4+ T cell subpopulations from Aire-Knockout Rats

The dataset consists of microarray gene expression data from four key CD4+ T cell populations—Tconv, Treg, Tfh, and Tfr—isolated from 7-month-old Aire-knockout rats with high levels of anti-IFNα autoantibodies and age-matched control rats. The cells were isolated from spleens and axillary lymph nodes using flow cytometry, with each population being sorted based on specific markers (CD3+ CD4+ CD25- ICOS- for Tconv, CD25+ ICOS- for Treg, CD25- ICOS+ for Tfh, and CD25+ ICOS+ for Tfr). RNA was purified from these sorted populations, and transcriptome analysis was performed using Clariom™ S Pico Assay HT gene expression chips.

Methods
Spleens and axillary lymph nodes were homogenized to create a single-cell suspension. Erythrocytes were lysed from splenic samples using an ACK solution. For transcriptome analysis, T cell populations were sorted based on specific markers (CD3+ CD4+ CD25- ICOS- for Tconv, CD3+ CD4+ CD25+ ICOS- for Treg, CD3+ CD4+ CD25- ICOS+ for Tfh, and CD3+ CD4+ CD25+ ICOS+ for Tfr) using the MA900 cell sorter. RNA was purified from the sorted cells, with quality assessed by the Agilent RNA 6000 Pico kit, and samples with a RIN >7.5 were selected for analysis. Transcriptome profiling was performed using the Genetitan MC machine on Clariom™ S Pico Assay HT gene expression chips.