Extended Data Fig. 3: Investigating the transcriptional response upon enhanced editing.

a, b, Fold change expression of cell cycle related genes relative to UT 24 h after AAV-based editing with the indicated treatments in CB (a) or mPB (b) HSPCs (CB: n = 8, 5, 7, 6, 3, 3, 3, 3; mPB: n = 4, 4, 4, 3). Median. c, Fold change expression of CDKN1A relative to UT 24 h after IDLV-based editing with indicated treatments in CB HSPCs (n = 3). Median. d, Fold change expression of CDKN1A relative to UT at 24 h after AAV-based editing with indicated treatments in CB HSPCs (n = 5). Median. e) MA plots showing significant down- (green) and up- (red) regulated genes after AAVS1 editing in mock electroporated (left) and standard edited (right) compared to UT (n = 3). PPP1R12C, the AAVS1 hosting gene appears among the downregulated genes, concordantly with previous reports showing transient transcriptional repression at the site of DNA DSB¹⁵. f) Random walk plots for the indicated Reactome categories. Relative adjusted p-values and NES are shown. g) Venn diagram showing the number of genes related to the “Allograft rejection” category upregulated upon standard editing and downregulated in presence of “+ Ad5-E4orf6/7” treatment. h) Venn diagram showing the number of HDR genes (“Homology directed repair” category from Reactome database) shared with E2F pathway target genes (Hallmark gene set) from cluster 1 or other clusters from Fig. 3e. i) Schematic of “cell cycle” and “p53 pathway” KEGG gene ontologies highlighting genes (red) belonging to clusters 1 (top) and 3 (bottom) of Fig. 3e. For all panels with statistical analysis: Friedman test with two-tailed Dunn’s multiple comparisons. n indicate independent experiments, except for Extended Data Fig. 3e where n indicates independent samples.