Fig. 1: Genome-scale CRISPR-Cas9 screen identifies PHF6 as a dependency in rhabdoid tumor cell lines.

a Two-class comparison of 10 biologically independent RT cell lines (blue) versus n = 886 biologically independent other cell lines (gray) plotted with CERES score for dependency on PHF6 on the x-axis. Negative CERES score demonstrates increased dependency. Statistical analysis was performed using a Benjamini–Hochberg corrected two-tailed Student’s t-test; P = 1.12 × 10 − 8. b Indel frequency assay. PHF6 was targeted with a guide RNA-Cas9 RNP in G401 RT cells and control Pfeiffer cells, and genomic DNA was harvested and sequenced after 7, 14, and 21 days. All indels were binned into in-frame (red) or out-of-frame (black). A non-targeting guide was used as a control. Data are represented from mean of three biological replicates. c, d Effects of PHF6 knockdown on proliferation of SMARCB1-deficient RT cell lines or (d) SMARCB1-expressing ES2 and MCF7 control cell lines. Data are represented from mean of n = 16 technical replicates per cell line per condition from one independent experiment. e Effects of exogenous re-expression of PHF6 following knockdown of PHF6 in G401 and TTC549 cells. Data are represented from mean of n = 8 technical replicates per cell line per condition from one independent experiment. Source data are provided as a Source Data file.