Supplementary Figure 14: Developmental arrest of T-cell maturation in Rag1 and Rag2 knockout mice at β-selection.
From: Inferring population dynamics from single-cell RNA-sequencing time series data
(a,b) Rag1 and Rag2 knockout mice have T-cell populations which are delayed in developmental progress along T-cell maturation measured with diffusion pseudotime compared to age-matched wild-type mice. The p-value is the result of the one-sided Kolmogorov-Smirnov (KS) test which was used to test whether the knock-out empirical cumulative density function of the knock-out lies below that of the wild type cells. (a) Rag2 knockout (Rag2KO) (n = 423 cells) and wild-type (n = 971 cells) samples at E14.5. (b) Rag1 knockout (Rag1KO) (n = 1565 cells) and wild-type (n = 2484 cells) samples at E16.5. (c,d) Mean marker gene expression by sample of age matched wild-type (WT) and Rag1/Rag2 knockout (Rag1KO, Rag2KO) embryos at E14.5 (c) and E16.5 (d). (e) Beta-selection point estimators by regularization parameter (reg). (f) Scatter plot of diffusion pseudotime coordinates obtained based on wild-type and on merged wild-type and mutant mouse samples. The dependency can be approximated with a smooth function (blue line: natural cubic spline fit of degree five). Yellow line: identity function.
