Figure 3
From: Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
Effect of detergent removal from the ATAC-seq protocol. (a) The fraction of mitochondrial reads in samples prepared without detergent was considerably smaller than those prepared with the original protocol. Treatment with anti-mt DNA CRISPR led to further decrease of mitochondrial reads (3.1-fold). (b) The fraction of unique, non-mitochondrial reads was considerably higher when detergent was not used. Surprisingly, the anti-mt DNA CRISPR treatment had only a marginal effect on the fraction of usable reads (1.1-fold increase). (c) At the same sequencing depth, only 1.1-fold more peaks were called in the ND treated samples. DT samples 18 and 19 were combined as in Fig. 2c. (d) ND samples displayed higher background (the number of non-mitochondrial reads outside peaks identified in any DT or ND sample). Numbers in blue above the bars are the ratio between number of reads in peaks and the number of background reads (signal/noise) (e) An example illustrating the higher background in ND samples, highlighted by the dashed boxes (chr6:420,146–448,555). Fold-differences calculated on medians.
