Extended Data Fig. 3: Delineating the ILC-γ/δ TCR thymocyte cluster and pro-apoptotic cluster from the main α/β TCR lineage pathway.
From: Pre-T cell receptor self-MHC sampling restricts thymocyte dedifferentiation
a. Distinguishing ILC-γ/δ-like cells from DN3b/4 in the DN4 libraries by gene expression. The heatmap on the left shows a manually curated panel of gene transcripts selected by likely high representation in either DN3b/4 or ILC-γ/δ-like cells. Log2 Fold-change (L2FC) and Padj in the DN4 libraries for differential expression between the DN3b/4 clusters and ILC-γ/δ-like clusters are shown in the volcano plot to the right with transcripts associated with ILC development are highlighted in light purple (Id2, Zbtb16, Gata3, Rora). TCR γ and δ transcripts are highlighted in green, and Trbv transcripts highlighted in blue. b. Gene expression profile of the pro-apoptotic cluster. The dominant pro-apoptotic cluster upregulated gene expression changes are similar between all the MHC+ libraries on comparison with the 2 dominant clusters within each of these libraries. All log2-fold changes (L2FC) are relative only to the 3 clusters listed in each heatmap (i.e. local) and not to the average across all clusters in that library.
