Fig. 2: Gene expression changes during spermatogenesis are largely transcriptional. | Nature Communications

Fig. 2: Gene expression changes during spermatogenesis are largely transcriptional.

From: RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis

Fig. 2

a Example windows for PRO-seq analysis in promoter (TSS to TSS + 150) or gene body (TSS + 250 to TES). b Scatter plot comparing the fold changes between SG and SC in RNA-seq versus PRO-seq gene body signal (TSS + 250 to TES). Spearman’s r = 0.85, and n = 19,823. c Scatter plot as in b, for the fold changes between SC and RS. Spearman’s r = 0.63, and n = 19,823. d Box plot representation of the distribution of fold changes in RNA-seq (empty box) or PRO-seq gene body (TSS + 250 to TES) (dotted box) for the SC to RS transition. Genes are grouped based on RNA-seq status as upregulated (red, n = 1134), unchanged (gray, n = 5880), or downregulated (blue, n = 12,226) as in Fig. 1e. Line represents median, box represents 25–75th percentile, whiskers represent 1.5X interquartile range. P-values from two-sided Wilcoxon signed rank test. e Heatmaps show relative RNA-seq (left, as in Fig. 1f) compared to relative PRO-seq gene body (TSS + 250 to TES) signal (right). n = 17,078. f–h Plots of average relative signal from RNA-seq (solid line and circle) or PRO-seq in gene bodies (dotted line and square) for each cell type, for clusters 1 (f), 4 (g), and 6 (h). Source data are provided as Source Data Fig. 2.

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