(A) Comparison of the transcript profiles of DN T cells and autologous SP T cells (combined CD4 and CD8 T cells) isolated from inguinal and axillary lymph nodes of gld mice as described in . The insets show purity and hallmarks properties of DN T cells including expression of TCR and B220 and lack of CD4 and CD8 on their surface. The Minus versus Average (MvA) plot shows intensity log-ratio M = log2 (DN/SP) versus mean log-intensity A = [(log2 (DN)+log2 (SP)]/2. Out of 32,000 transcripts examined, expression of 160 genes was at least 3-fold higher in DN than in SP T cells. Highly expressed genes including junctional adhesion molecules, hydrolyase enzymes, and apoptotic death molecules are highlighted. Selected under-expressed genes in DN T cells relative to SP T cells are also highlighted. (B) Validation of expression of selected genes by real-time PCR. Expression level of each gene was normalized relative to expression of 18 s rRNA in the same cell subset. X-axis shows -fold change in expression of indicated genes in DN T cells relative to SP T cells. (C) Validation of specific expression of sdc1 by flow cytometry. Splenocytes were isolated from 16-week-old C3H-gld/gld mice, stained with APC-TCRβ, PerCP-CD4, FITC-CD8α, and PE-sdc1 or with APC-TCRβ, PerCP-CD4, FITC-CD8α, and PE-B220 mAbs and analyzed by FACS. Dot plot: TCR+ cells were gated followed by specific gating of DN (R5), CD4+ (R3), and CD8+ (R4) subsets. Histograms: Overlays show relative expression of TCR, B220, and sdc1 by gated CD4, CD8, and DN subsets.