The transcription factor Gli3 promotes differentiation from double positive to CD4 single positive thymocyte by repression of Shh

We used Affymetrix microarrays to understand the genome wide differences in Wildtype and Gli3 mutant (Gli3+/- and Gli3-/-) (n=2) embryonic day 18.5 DP CD69-, DP CD69+ and SP4 thymocytes. Wildtype and Gli3 mutant (Gli3+/- and Gli3-/-) (n=2) embryonic day 18.5 fetal thymus were sorted for DP69- (CD4+CD8+CD69-), DP69+ (CD4+CD8+CD69+) and SP4 (CD4+CD8-) cells. RNA extracted from these cells was sequenced to help understand the transcriptional changes governing DP to SP thymocyte differentiation and selection in the Gli3 mutant.