Influence of histone lysine demethylase JMJD2-specific inhibition on the senescence-associated secretory phenotype developed in human stromal cells upon DNA damage

Recent advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this epigenetic study to streamline the transcriptome profiling (RNA-seq) of human stromal cells developing a typical senescence-associated secretory phenotype (SASP) upon stress induced by DNA damage or DNA damage together with pharmacological targeting of JMJD2, a trimethylation-specific demethylase of histone H3K9 and H3K36. Overall transcript profiles of human primary prostate stromal cells (PSC27) were generated by deep sequencing in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays