Gene expression profiling and whole genome methylation analysis of the Setd2-deleted NHD13 HSPCs. (A) RNA-seq and Gene Set Enrichment Analysis of the BM HSPCs of the WT, NHD13/Setd2f/f, and NHD13/Setd2Δ/Δ mice at 4 weeks after poly(I:C) injection. (B) Gene expression profiles revealing the differentially expressed genes in the pathways regulating the G2M checkpoint, HSC maintenance and differentiation, erythrocytes, megakaryocytes, apoptosis, and NF-κB targets. (C) qPCR analysis of representative genes of interest, which are labeled with red boxes in panel B. (D) Comparison of relative methylation differences between the BM HSPCs of the NHD13/Setd2f/f and NHD13/Setd2Δ/Δ mice at 4 weeks after poly(I:C) injection. Each dot represents a methylation locus that was detected >10 times. (E) Number of hypomethylated (2792) and hypermethylated (4992) DMRs. Each dot represents a DMR. (F) Comparison of average methylation levels of all DMRs between the NHD13/Setd2f/f and NHD13/Setd2Δ/Δ BM HSPCs. *P < .05; **P < .01; ***P < .001; ****P < .0001.