Extended Data Fig. 4: Supplementary Data for Fig. 4.

a) Line plot showing the fraction of reads (y axis) containing a deletion at the indicated position across the HS2 region (x axis), with expected cut sites for each sgRNA indicated with red dotted lines. b) The number of deduplicated reads (y axis) per genotypes (x axis) from HS2 CRISPR deletions. In the HS2 Cas9 TDAC-seq sgRNA tiling library, 541 genotypes have at least 400 reads (red line). c) 2D histogram of UMIs plotted by the number of reads of the most abundant CRISPR genotype per UMI (x axis) and all genotypes (y axis). Both values would be equal for pure UMIs, indicated by red boxes along the diagonal. Data are representative of a sample of 10,000 sequencing reads. d) Heatmaps of TDAC-seq using CRISPR-Cas9 cutting on the HS2 enhancer in K562 cells. Individual sequencing reads were assigned to one of 541 genotypes (y axis), with black lines indicating the CRISPR deletion position and length on the HS2 region. For each genotype, the average number of DddA11 edits in a 100-bp sliding window is shown across the HS2 region (x axis). e) Heatmap showing the statistical significance (Welch’s two-sided t-test) of comparing DddA11 accessibility between reads that contain a deletion spanning the entire deletion window and all other reads. This value is calculated for all possible deletion windows indicated by their start position (horizontal axis) and length (vertical axis). Those with less than 100× coverage were excluded. Arrow indicates a 10-bp deletion window corresponding to the minimal key motif discussed in Fig. 4. f) The proportion of reads from gDNA with and without CRISPR deletions after individual transduction of sgRNA-1 and sgRNA-11 into K562 cells. Data in a-e are representative examples of n = 2 replicates. Correlation between TDAC-seq replicates is presented in Supplementary Fig. 3. Experiments for data in f were performed once.