CRISPR Knockout Screen to Identify Mechanisms of Rescue of DDX41-deficient Hematopoietic Progenitors

DDX41 is essential for the survival and proliferation of mouse hematopoietic progenitor cells (HPC). To identify mechanisms to rescue the survival of DDX41-deficient HPC, we conducted a genome-wide CRISPR Knockout Screen in DDX41-deficient and wild-type mouse bone marrow lineage-negative cells. Overall design: Lineage-negative BM were harvested from wildtype or Ddx41-floxed mice expressing Cas9 from one Rosa locus and Cre-ERT from the other Rosa locus. The cells were transduced with the Brie lentiviral CRISPR library and allowed to proliferate in liquid culture for 5 days. The surviving cells were harvested and their DNA was isolated in order to identify the gRNA that were over and under-represented in DDX41-deficient cells compared to control cells.