Extended Data Fig. 8: Assessing relationships of T_H1 and Tfh-lineages with T_CM, GC Tfh and Tr1 subsets in the GPfates model.

a, Visualisation of Sell and Ccr7 expression on 2D bGPLVM representations overlaid with OMGP trajectories representing T_H1 or Tfh branch. b, Co-expression of Sell and Ccr7 along pseudotime, for all cells annotated for the Tfh (left) or T_H1 (right) branch as outlined in methods. Kernel density estimation failed to estimate a population of Sell⁺ Ccr7⁺ cells, hence a threshold was estimated where cells express both Sell ≥ 4.7 and Ccr7 ≥ 3.75 corrected gene values. c, Representative FACS plots and graph showing expression of T_H1-markers (CCL5 and CXCR6) on PbTIIs at D28 p.i. isolated from the spleen and inguinal lymph nodes of the IAT group. Experiment performed once (n=6 mice). Statistical test performed using Wilcoxon matched-pairs signed-rank test. p-value where indicated is *p<0.05. d, Visualisation of Pdcd1 expression on 2D bGPLVM representations overlaid with OMGP trajectories representing T_H1 or Tfh branch. e, Co-expression of Pdcd1 and Ccr7 along pseudotime, for all cells annotated for the Tfh branch. Kernel density estimation failed to estimate a dense population of Pdcd1⁺ Ccr7⁺ cells, hence a threshold was estimated where cells express both Pdcd1 ≥ 4.0 and Ccr7 ≥ 3.50 corrected gene values. f, Visualisation of Il10 and Ifng expression on 2D bGPLVM representations overlaid with OMGP trajectories representing T_H1 or Tfh branch. g, Co-expression of Il10 and Ifng along pseudotime for all cells annotated for T_H1. Tr1 cells are annotated as those cells expressing Il10 and Ifng above the threshold drawn (cells expressing both Il10 ≥ 4.9 and Ifng ≥ 3.75 corrected gene values), according to kernel density estimation.