Fig. 2

Transgenic insertion sites of four random integrations of a PPM1D-transgenic construct in mice as detected with TC-hunter. Results from TC-hunter of the best TIS for each sample analyzed (A-D). The circular representation shows the genomic region of the TIS in the host (bottom gray semicircle) and the genomic sequence of the transgenic construct (upper red semicircle). The different genomic features of the transgenic construct are depicted as black rectangles with their corresponding annotation. The histograms (in gray) show the sequencing coverage at the specified genomic regions. Discordant read pairs are shown as red lines, while chimeric reads are shown as black lines. The IGV snapshots show the supporting reads at the TIS in the construct (upper panel) and host (lower panel). Only chimeric reads are shown in both panels. These are grouped and colored by the chromosome of the mate; red arrows point to the validated breakpoints (BP1 and BP2) in the host. A TIS from sample 41. The construct panel shows the 2 predicted TIS. M41-1 corresponds to the best scoring TIS. M41-2 despite having a high score (8.011), could not be experimentally validated. B TIS from sample M42. Discordant pairs (in red) bisect the chimeric reads (in black) suggesting that the construct is inserted in the opposite direction with respect to the host. The TIS region spans over 29,531 bp. C TIS from sample M45. The TIS region span over 56,720 bp and the circular plot suggest a reverse insertion of the transgene. D TIS from M47. The transgene is also inserted in the opposite direction with respect to the host