RNA sequencing of control and Dnmt1?/?ep knockout keratinocytes at P3

To investigate whether the effects of DNMT1 ablation in keratinocytes are cell-autonomous in the context of the innate immune response, RNA sequencing was performed using keratinocytes isolated from P3 Dnmt1?/?ep and control mice. Overall design: For RNA sequencing epidermis of three control and three Dnmt1?/?ep mice was isolated at P3 and keratinocytes were cultured for 5 days. RNA was and then used for RNA sequencing. The aim was to do the analysis of differentially expressed genes across the two conditions to determine whether the effects of DNMT1 ablation in keratinocytes are cell-autonomous in the context of the innate immune response. Genes that showed a minimum of a 2-fold change in expression levels (adjusted P value of£0.05) were classified as up-regulated, whereas genes displaying a fold change of £ 0.5 (adjusted P value of£0.05) were categorized as down-regulated. The cutoffs for differential expression were set as absolute fold-change >2 and a corrected P-value of >0.05.