We measured intensity of Ptch1 staining in cilia of NIH-3T3 cells by double-labeling with antibodies to Ptch and Arl13b (a small GTPase that localises to cilia; see Caspary et al., 2007), and saw a dramatic reduction when we added ShhN, as expected (supplementary material Fig. S6).
We see that performances of ideal clusterings are excellent when compared with the appropriate grouping, as expected (Supplementary Fig. S2).
When we examined whether the Helitrons preferentially inserted into or near genes, we discovered that their frequencies within introns and >1 kb from genes were significantly higher than expected (Supplementary Fig. S6), suggesting the silkworm Helitrons preferential insertion into these regions.
We found that 21/42 of these genes showed distinct upregulation in the area around the regenerating pharynx, as expected (Supplementary file 1B; Figure 2 figure supplement 3).
The injection of Ad-VEGF increased the vascularity of the ischemic GC muscles as expected (Supplementary Fig. 16).
All of the strains were tested for their lecithinase activity in vitro and behaved as expected (Supplementary Fig. 6).
The root mean square fluctuations (RMSF) also displayed very similar dynamics, except for the loop regions, as can be expected (Supplementary Fig. S1B).
The time between correct high-confidence responses was well described by an exponential distribution (R2=0.98) suggesting these correct events occur randomly in time, as expected (Supplementary Fig. 5a).
Analysis of the reaction product with a Fragment Analyzer showed that longer repeat sizes were more heterogeneous, as expected (Supplementary Fig. S3A).
This simple analysis is in line with all of our experimental observations (Fig. 2a) with two notable exceptions, Fe and Ni, which exhibit less dynamic behaviour than expected (Supplementary Fig. 6).
This enhanced band B as expected (Supplementary Figure S1A).
