Fig. 1.

Detection of RNA editing on mouse brain tissue by padlock probes and in situ sequencing. a Workflow for the detection of edited and unedited transcripts and sequencing of the barcode by in situ sequencing. b Representative image of the DAPI staining of cell nuclei in a coronal section from an adult brain. The arrows in the schematic illustrations of mouse brains at different developmental stages indicate the bregma coordinate from where the coronal sections were obtained. The regions selected for the regional analysis are outlined in adult brain and were selected based on the reference image from the Allen Brain Atlas. Regions of interest (ROIs) were manually outlined in the tissue image for each replicate. c Whole brain editing data, the mean of all replicates per developmental stage (Additional file 5), for each edited site in a bubble chart, derived from raw ISS reads in Additional files 7, 8, 9, and 10. The color of the bubbles indicates the editing level and the size of the bubble the level of expression for each transcript. Lowly expressed targets (< 500 reads) were excluded from further analysis and are not shown here. d Representative images for the results from one brain section from an adult mouse showing the spatial distributions of edited (orange) and unedited (cyan) transcripts of Cyfip2, Unc80, and Blcap. Each dot represents one transcript. e Representative images of the regional editing levels in one brain section from adult mouse for Cyfip2 K/E, Unc80 S/G, and Blcap Y/C, where the color of the region indicates the level of editing. The scale bar is 1 mm in all images