Also, a few new DMS modification sites were found under such condition, suggesting changes in local structure due to protein binding.
Using this algorithm 23,737 A-to-G modification sites were found in the squid coding regions, compared to only 2933 non A-to-G modifications.
Out of 703 substitution sites found in tRNAs, 604 sites (86%) can be accounted for by the 6 known base modifications discussed above.
In 45CBS, we identified 50 labeled residues in total, and we found only 4 modification sites which were not detected in wtCBS (Table 2).
De-novo sequencing, through the aide of Prospector Product software (prospector.ucsf.edu), was also performed for either confirmation of modification sites reported by MASCOT or to find other modification sites which MASCOT might fail to determine.
Unfortunately, we could not find peptide fragments with clear modification sites.
We found that compared with ChIPDiff, QChIPat identified fewer differential histone modification sites (DHMSs).
We found 213 modified peptide matches consisting of 75 unique known modification sites before and 232 modified peptide matches and 81 unique modification sites after applying PTMClust, for an overall improvement of ∼9%.
Further, to consider the potential influence of off-target gene modifications (Yee, 2016), we detected the most probable ten off-target modification sites which were designed at the CRISPR website (http://crispr.mit.edu/) (Table S3) and found that there was no off-target gene modification (Fig. S2), which excluded the potential influence of off-target gene modifications.
To consider the potential influence of off-target gene modifications (Yee, 2016), we detected the most probable ten off-target modification sites which were designed at the CRISPR website (http://crispr.mit.edu/) (Supplemental Table. 3) and found that there was no off-target gene modification (Supplemental Fig. 2), which excluded the potential influence of off-target gene modifications.
