Fig. 2: Spatial total RNA-sequencing of regenerating skeletal muscle.
From: Spatial mapping of the total transcriptome by in situ polyadenylation
a, H&E histology of mouse tibialis anterior muscles collected 2, 5 and 7 dpi. b, Clustering of spot transcriptomes based on total transcriptome repertoires (Methods). c, Differentially expressed RNAs across regional clusters. The y axis shows log-normalized expression of each feature. Mean expression across each cluster is reported, colored according to the legend in b. Error bars show s.d. Reported statistics to the right of plots reflect differential gene expression analysis performed across clusters on merged STRS samples (n = 4,257 spots from four tissue sections; two-sided Wilcoxon Rank-Sum test; Methods). Asterisks next to transcript names reflect differential expression analysis performed across skeletal muscle Visium (n = 2,806 spots from three tissue sections) and STRS samples showing adjusted P value (Padj) (**Padj < 10-50, ***Padj < 10–150; two-sided Wilcoxon Rank-Sum test; Methods). FC, fold change. d, Spatial maps for select features from c. Color sale indicates log-normalized expression, or that the transcript was not detected (gray). e, Average detection of miRNAs compared between small RNA-sequencing (n = 8) and STRS (n = 4). Axes show log2 counts per million transcripts, normalized to the total number of transcripts that map to small RNA loci with miRge3.0 (Methods). The top 100 most abundant miRNAs detected by small RNA-sequencing are shown. Line shows a linear regression and 95% confidence interval. f, Spatial maps of mature miRNA expression detected by STRS. Color scale shows log-normalized miRNA counts, quantified by miRge3.0. Gray indicates spots in which the transcript was not detected.
