PCR array analysis of gene transcription in control and anti-CD3–treated Rag1−/− and Gli2ΔC2Rag1−/− thymocytes. Bars show average fold change in gene transcription on anti-CD3 treatment, relative to transcription in untreated samples. Values were calculated by dividing the average gene transcription in the treated samples (Rag1−/− + anti-CD3 or Gli2ΔC2Rag1−/− + anti-CD3) by the corresponding ones from the control samples (Rag1−/− or Gli2ΔC2Rag1−/−). (A,B) All genes shown exhibited statistically significant change after anti-CD3 treatment in Rag1−/− and/or Gli2ΔC2Rag1−/− thymocytes. (A) Genes significantly up-regulated after anti-CD3 treatment. P values for Rag1−/−: Nrip1, P = .02; Tcf7, P = .06; Birc3, P = .02; Fasl, P = .04; Nab2, P = .002; and CD5, P = .004. P values for Gli2ΔC2Rag1−/−: Nrip1, P = .005; Tcf7, P = .03; Birc3, P = .5; Fasl, P = .4; Nab2, P = .04; and CD5, P = .02. (B) Genes significantly down-regulated after anti-CD3 treatment. P values for Rag1−/−: CD25, P = .002; Tert, P = .07; Myc, P = .01; Cdh1, P = .04; Birc1a, P = .05; Brca1, P = .007; p53, P = .1; Hoxa1, P = .005; and Wnt1, P = .03. P values for Gli2ΔC2Rag1−/−: CD25, P = .01; Tert, P = .01; Myc, P = .06; Cdh1, P = .08; Birc1a, P = .2; Brca1, P = .04; p53, P = .04; Hoxa1, P = .2; and Wnt1, P = .3. (C) Change in transcription of FoxA2 after anti-CD3 treatment. Difference in change in transcription of FoxA2 was significant between genotypes, P = .05.
