Transcriptional Changes during T cell development following conditional loss of Bcl6
In this study we investigated the changes during T cell development in Rag knockout Bcl6 conditional knockout E16.5 thymi compared to Control E16.5 thymi.  We measured the transcription changes by RNA seq in three different populations including CD25+, CD8+CD4- (ISP) and CD8+CD4+ (DP) thymocytes. Overall design: Embryonic day (E16.5) thymi from Rag knockout Bcl6 conditional knockout (Ragfl/flBcl6LckCre) embryos were used for this study. CD25 positive thymocytes were isolated from Control (RagKOBclfl/flLckCre-) and RagKOBcl6coKO (RagKOBcl6fl/flLckCre+). Some RagKOBcl6coKO thymi were treated with anti-CD3 for 2days to promote differentiation following a TCR mimicking stimulus. CD8+CD4- (ISP) cells and CD8+CD4+ (DP) cells were isolated from these treated thymi. RNA-Seq was carried out on the CD25 positive, ISP and DP populations from Control and RagKOBcl6coKO samples.