Extended Data Fig. 2: Protec-seq results in robust and high quality DSB maps.
From: Spo11 generates gaps through concerted cuts at sites of topological stress
a, Biological repeats as well as samples with similar phenotype show high correlation at 10-nt resolution. 5′ end log2-transformed counts are shown. The corresponding Pearson correlation coefficients (R) are indicated in the bottom right corner of the scatter plots. The compared samples and time points are indicated at the left and bottom axes. Top right, to test whether the differences between rad50S and wild-type are mainly due to differential degradation, sub-samples of rad50S dDSB fragments were selected according to the dDSB length distribution of wild-type cells. The resulting improvement of R from 0.88 (for unselected rad50S versus wild-type dDSB) to 0.93 supports this assumption. b, Positional overlaps of dDSB 5′ ends with Spo11-oligo 5′ ends with 1 nt tolerance. OO, both dDSB fragments ends overlap; ON, one end overlaps; NN, both ends do not overlap. Filled bars represent total fragment counts as a percentage of the total; empty bars represent deduplicated counts. The last panel shows the percentages of the Spo11-oligo sample overlapping with wild-type dDSB (O, overlap; N, no overlap). All samples are from 4 h in SPM (t4). c, dDSB fragment and Spo11-oligo profiles from chromosome III. Genome-wide Pearson correlation coefficients with the wild-type t4 profile at a resolution of 10 nt are indicated on the right side of each panel. d, Left, frequency of (d)DSB sites of certain depths (log10 bins) as a percentage of total recovered break sites. Right, the frequency of (d)DSBs of certain depths (log10 bins) as a percentage of total (d)DSBs. The depths are binned into 1, 2–10, 11–100, 101–1000, 103+1–104, 104+1–105. All samples are from t4.
