Extended Data Fig. 9: Characterization of the Foxn1-deficient thymic rudiment.
From: Developmental trajectory and evolutionary origin of thymic mimetic cells
a, Visualization of expression changes between Foxn1−/− mice and non-transgenic wildtype mice. Each line represents a gene of the indicated signature and its position on the x axis shows the value of the t statistic derived from differential expression analysis. Numeric values listed in the left column represent log10(adj. p) from enrichment analysis with camera25. Log transformed p values of upregulated sets were multiplied with −1 so that positive values indicate upwards directionality, and negative values indicate downwards directionality, respectively. b, RNA in situ hybridization of consecutive sections developed with the pharyngeal marker gene Pax9 and the TEC-specific marker gene Foxn1 at P14. Note that some patches of the Pax9-positive epithelium lack Foxn1 expression, indicating cellular heterogeneity of the Foxn1−/− epithelium; scale bars, 0.1 mm. Representative for n = 4 mice with similar results. c, snRNAseq data from nuclei of thymus tissue from Foxn1+/− (n = 3) and Foxn1−/− (n = 6 mice, pooled in n = 3 samples of two animals each). UMAP of all nuclei after data processing, clustering and annotation. Broad cluster identities are labelled. d, Zoomed in view on the ionocyte cluster from c; each dot represents a cell, with the genotype of origin indicated by colour (left panel). Expression levels for Foxi1 (right panel). Expression values are log2(normalized counts). e, Contributions of individual samples to clusters from d. Genotypes are coloured and replicates are are identified by different colour hues. f, Signature scores (AUCs21) for the indicated mimetic cell signatures in the UMAP of c.
