Expression data from meduallar thymic epithelial cells and thymic or splenic B cells. Mus musculus

Aire is a transcriptional regulator that induces promiscuous expression of thousands of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells. Overall design: Mature EpCAM+MHC-II high mTECs, Immature EpCAM+MHC-II low mTECs, and EpCAM+Ly51+ cTECs were flow-sorted from thymi isolated from thymi of C57BL/6 6weeks old mice. CD19+Aire.GFP+ thymic B cells and CD19+ Splenic B cells were flow sorted from thyme or spleen, respectively, of C57BL/6 Adig 6weeks old mice. Typically, 3 mice were pooled to obtain 30-60 thousand sorted TECs or thymic B cells, which were then analyzed by gene expression profiling. Specifically, total RNA was extracted from ~30,000 pooled sorted cells using Trizol. Purified total RNA was then amplified using the MessageAmp RNA kit (Ambion). Biotinylated cRNA was then hybridized to Affymetrix Mouse Gene 1-ST arrays by the genomics core at the Weizmann Institute.