Bulk ATAC-seq for 12 RUNX1 variants including WT and LOF controls

Here, we deploy SEUSS, a Perturb-seq method, to generate mutations on RUNX1 and measure the impact of 10 RUNX1 Runt domain missense mutations on the RUNX1 regulon in myelogenous leukemia cells (K562) with bulk ATAC-sequencing. WT and LOF controls are included. We generated a clonal K562 cell line with doxycycline-inducible CRISPRi knockdown of endogenous RUNX1 (~70% reduction). Bulk screen was performed for each variant (12 elements in total) separately in K562 cells grown in doxycycline to induce repression of endogenous RUNX1 and hygromycin to select for transduced cells. Each variant contains three biological replicates with ~100,000 cells. At day 7 post transduction, bulk ATAC libraries were prepared and sequenced using the 10X Genomics Chromium platform.