Fig. 1: Development of mouse thymic mimetic cells.
From: Developmental trajectory and evolutionary origin of thymic mimetic cells
Enrichment of canonical TEC and mimetic signatures in bulk RNA-seq data of purified TECs from E15.5 (n = 4) and P1 (n = 2) time points compared with the P28 (n = 3) time point. a, Visualization of changes in gene expression between conditions. 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(adjusted P) from enrichment analysis with camera25. Log-transformed P values of upregulated sets were multiplied by −1 so that positive values indicate upwards directionality and negative values indicate downwards directionality. b, Log-transformed and signed P values from camera (two-sided, Benjamini–Hochberg adjusted) as shown in a, represented as a heat map. Values beyond the limits of the colour scale were rounded to the nearest limit. Adj., adjusted. c, Overall Foxn1 expression levels (log2 of counts per 10,000 reads (CP10K)) in Aire-stage cells and mimetic cells from scRNA-seq data (n = 4 mice; age, P28). The proportion of cells with detectable Foxn1 is indicated; P = 1.2 × 10−33 (two-sided binomial test, Benjamini–Hochberg adjusted). d, Proportion of cells with detectable CRISPR–Cas9-induced barcodes at the Hprt locus for each signature. n indicates total number of cells, pooled from three mice at P28. Data are mean ± 95% confidence interval of proportions (Wilson/Brown method51); P values are derived via likelihood ratio test between logistic regressions with or without ‘signature’ as a predictor.
