(J) Representative profile of peaks on chromatin 5 that were identified by YTHDC1 ChRIP-Seq of HEK293T cells with or without Zeocin treatment. (K) Quantification of (J), showing the number of peaks identified by YTHDC1 ChRIP-Seq. The value is the average of two independent experiments. ...
To calculate the distribution profile of DNA:RNA hybrids enrichment at DSBs, the log2 ratio values calculated for each 50 bp bin for DRIP-seq reads were intersected to five distance intervals from the top 50 cut AsiSI sites (determined in our laboratory50): 0–0.5, 0.5–1, 1–1.5, ...
In an effort to understand the mechanism of BLM recruitment at the DSBs, we treated U2OS–AsiSI–ER cells with 4-OHT for different time intervals upto 4 h (details of all treatments in the recruitment phase in Supplementary Figure1A). The extent of DSBs increased with time as indicated bo...
The complete profile creation script was deposited in Github as 03.DSB.profile.sh. The deepTools [44] 3.2.0 package was used to perform the replicate consistency check. High correlation coefficients (Pearson’s r = 0.88 and Spearman’s ρ = 0.93) suggest that the replicates were consistent ...