Crystal violet staining and clone counting

Media was aspirated from 10 cm plates before fixation with 1 mL freshly diluted 4% paraformaldehyde in 1× DPBS for 15 min at RT. Fixative was removed and 1 mL 0.5% w/v crystal violet solution (Thermo Fisher Scientific, Cat. # C581-25) dissolved in 20% methanol in water was applied to each plate and incubated for 30 min at RT. Crystal violet was removed and plates were washed 2× with deionized water before drying overnight at RT. Dried plates were photographed and crystal violet stained clones were counted manually using FIJI (Schindelin et al., 2012).