Differential expression analysis of sense transcripts. Reads were mapped to a human (hg38) + HSV genome and read counts for each gene was calculated using STAR.

ComBat was used to correct for batch effect and DESeq2 was used to normalize counts and calculate differential expression for reads that map to the sense strand. Genes with an adjusted p value < 0.05 and a fold change > 2 or < -2 are reported. ATRX_UP: Genes upregulated in ATRX KO cells infected with HSV 7134 at 8 hpi compared to uninfected ATRX KO cells. ATRX_DOWN: Genes downregulated in ATRX KO infected with HSV 7134 at 8 hpi cells compared to uninfected ATRX KO cells. CTRL_UP: Genes upregulated in Control cells infected with HSV 7134 at 8 hpi compared to uninfected Control cells. CTRL_DOWN: Genes downregulated in Control cells infected with HSV 7134 at 8 hpi compared to uninfected Control cells. inf_UP: Genes upregulated in ATRX KO cells infected with HSV 7134 at 8 hpi compared to Control cells infected with HSV 7134 at 8 hpi. inf_DOWN: Genes downregulated in ATRX KO cells infected with HSV 7134 at 8 hpi compared to Control cells infected with HSV 7134 at 8 hpi. No genes met the p value and fold change cutoff, so this list is not reported. uninf_UP: Genes upregulated in uninfected ATRX KO cells compared to uninfected Control cells. uninf_DOWN: Genes downregulated in uninfected ATRX KO cells compared to uninfected Control cells.
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