Fig. 3

Transcription-coupled repair in mouse lemur and human fibroblasts. Average profiles of CPD XR-seq (top) and (6–4)PP XR-seq (bottom) over 5277 and 3366 annotated genes are plotted for human (left) and mouse lemur (right), respectively. Transcription start sites (TSS) and transcription end sites (TES) were retrieved from GTF (Gene Transfer Format) files for the two genomes. Transcribed (red) and nontranscribed (blue) strand repair are shown in the downstream and upstream of TSS and TES, respectively. 10 kb upstream and downstream of TSS and TES were divided into 100 bp windows. XR-seq reads aligned to each bin were normalized to RPKM (reads per kilobase per million mapped reads). The XR-seq RPKM values were normalized by the shuffled RPKM values derived by mapped reads aligned to random genomic sites. Only replicate 1 is shown. TS/NTS median values for TSS downstream for CPD are 1.76 and 2.31 for human and mouse lemur, respectively