Effect of autophagy inhibition (ATG7/13 KD) on the transcriptome of proliferating and senescent cells
To identify differentially expressed genes by autophagy inhibition during cellular senescence, we performed transcriptional profiling by RNA sequencing (RNA-seq) with or without autophagy inhibition (using a shRNA targeting either ATG7 or ATG13), before and after senescence induction using a stress-induced senescence model (bleomycin-induced senescence) Overall design: IMR90 cells were treated with bleomycin (10 ug/ml for 24 h) to induce senescence. Autophagy was inhibited by expression of a shRNA targeting either ATG7 or ATG13 in proliferating cells and senescent cells. Total RNA was isolated using the acid phenol extraction method. One microgram of high-quality RNA samples (RIN > 7.0) was used to construct RNA-seq libraries using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). RNA-seq was performed on an Illumina NovaSeq 6000 sequencer.