Fig. 5
C-myc knockout NK1.1− IELPs show developmental arrest after agonist selection. a–h Flow cytometric analysis of thymic NK1.1− IELPs from 6- to 16-week-old TBGR C-mycΔ/ΔCd4 mice and TBGR C-mycfl/fl littermate mice as controls. Dot plot shows T-bet vs. CD122 (a), Qa2 (c), H2-Kb (e), and PD-1 expression (g). Numbers denote the percentage of cells in the gate (Mean ± SEM) for at least six mice per genotype. Bar diagram shows statistical analysis of (Mean ± SEM) T-bet vs. CD122 (b), Qa2 (d), H2-Kb (f), and PD-1 expression (h) in NK1.1− IELPs. i t-SNE map representing RaceID3 clustered cells from TBGR C-mycΔ/ΔCd4 and TBGR C-mycfl/fl littermate mouse as controls. Note that owing to the absence of T-bet+ IELPs in C-mycΔ/ΔCd4 mice only T-bet− cells are analyzed and shown for these samples. j t-SNE map showing the sample information of RaceID3 clustered cells. Bar diagram shows the relative contribution of individual samples to the seven different clusters identified by RaceID3. k, l t-SNE representation of the selected genes corresponding to relevant markers upregulated in T-bet− TBGR C-mycfl/fl (Cdk4, Eif5a, and Eef1b2 (k)) or T-bet− TBGR C-mycΔ/ΔCd4 (Bcl2, Ikzf2, and Nr4a1 (l)) IELPs within the different clusters as shown in i. m MA plot of differential expression analysis between CD122+T-bet− cells from TBGR C-mycΔ/ΔCd4 mice (top) versus CD122+T-bet− cells from age-matched (2–3 weeks old) TBGR C-mycfl/fl control mice (bottom). Differentially expressed genes involved in agonist selection, translational initiation, and C-Myc target genes involved in cell-cycle regulation and energy metabolism are highlighted. The ensemble of all Rps, Rpl, Rik, Gm, and RP genes are not displayed in the MA plot; please refer to Supplementary Fig. 4e. Bonferroni adjusted p value < 0.05
