I’m new here and I have one question about the experimental design:
For a given cell line X, are all CRISPR-Cas9 all genes are put together in the cell line X OR is it one CRISPR-Cas9 guide by gene on cell line X. (One gene at a time on X1 then another gene in the same cell line X2 (technical replicates of cell line X vs or all genes guides in the same cell line X)
Hello and welcome! The former is true, all genes in the Avana library are knocked out in a given cell line replicate. Please refer to Dempster et al. 2019 Figure 1A (and Supplementary Methods) for a description of the Achilles Pipeline’s experimental setup.