Transcriptome profiling of medullary thymic epithelial cells from Aire-knockout rats

This dataset contains transcriptome profiling data of thymic stromal cells from Aire-deficient and control rats. The thymic stromal cells were sorted into three fractions based on the expression of EpCAM, CD45, UEA1, and MHC markers: cTEC (Epcam+ CD45- UEA1low MHClo), mTEClo (Epcam+ CD45- UEA1med MHCmed), and mTEChi (Epcam+ CD45- UEA1high MHChi). RNA was extracted from these sorted cells, and RNA quality was assessed, with samples having a RIN >7.5 used for further analysis. The transcriptome analysis was performed using an Affymetrix GeneTitan MC system and Clariom™ S Pico Assay HT chip. The data for the mTEChi fraction are provided as .CEL files, which can be used for downstream gene expression analysis.

Methods
The thymi were minced, gravity-sedimented, and enzymatically digested to enrich for stromal cells. These cells were then sorted into three populations—cTEC, mTEClo, and mTEChi—based on the expression of specific markers (EpCAM, CD45, UEA1, and MHC). RNA was extracted from the sorted cells using the RNeasy Micro kit, and RNA quality was assessed using the Agilent RNA 6000 Pico kit. Only samples with a RIN >7.5 were used for transcriptome analysis. Gene expression profiling was performed using the Affymetrix GeneTitan MC system and Clariom™ S Pico Assay HT chip, and the resulting data for the mTEChi population are provided as .CEL files for further analysis.