Fig. 5

A Normalized expression values in the crisprQTL screen for cells with targeting (TGT) gRNAs (red) versus non-targeting (NT) controls (gray) for the four E2G links selected for orthogonal validation. B Schematic of experimental approach used to induce targeted element deletions in primary CD4.⁺ T cells, using gRNA/Cas9-nuclease ribonucleoprotein complexes (RNPs). The efficiency of the deletions was analyzed by PCR and automated electrophoresis. The perturbation-induced transcriptomic changes were assessed by bulk RNA-seq. C Automated electrophoresis analysis via TapeStation of the PCR products obtained after amplifying the targeted region in non-targeting (NT) control samples and CRISPR-deleted samples for four enhancer elements, across two donors (D1: donor 1; D2: donor 2). The size of the expected wild-type band is shown in brackets for each enhancer perturbation. D Normalized expression values for the DEG identified in the crisprQTL screen (A) in bulk RNA-seq data from cells with CRISPR deletion of the corresponding enhancer or with a NT control, across two donors. All four genes show the expected downregulation of expression, and three reach statistical significance (*adjusted p-value < 0.05)