Improved cytosine base editors generated from TadA variants
After 4 d of incubation, gDNA from HEK293T cells was harvested from the cells using 100 μl of Quick Extract DNA Extraction Buffer in accordance with manufacturer protocols. For allogeneic T cells, 50 μl of Quick Extract DNA Extraction Buffer was used on 1 × 10cells at 5–6 d post-transfections. Genomic DNA samples from mammalian cell samples were amplified with primers for site-specific genomic DNA amplification containing adapter sequences compatible with Illumina’s TruSeq HT system .
For the odds ratio plots, a single representative cell from the untreated clonally expanded cells is required as a reference point to compare with both the treated and untreated cells for both C-to-T and A-to-G deaminations. This cell was selected by ordering the untreated cells by proportion of A-to-G mutations and proportion of C-to-T mutations and selecting the one cell closest to the median for both metrics.
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