mRNA expression profiling of wild-type and ABCA1 knockout IMR90 cells during DNA damage-induced senescence

We have generated ABCA1 knockout cells using CRISPR/Cas9 system and expanded single cell clones for gene expression profiling. To identify differentially expressed genes during cellular senescence in wild-type and ABCA1 knockout cells, we performed transcriptional profiling with RNA sequencing (RNA-seq) before and after senescence induction using a stress-induced senescence model (bleomycin-induced senescence). Wild-type and ABCA1 knockout IMR90 cells expressing hTERT were treated with bleomycin (10 ug/ml for 24 h) to induce senescence, and total RNAs from proliferating (-bleomycin) and senescent (+bleomycin, 7 days after exposure to bleomycin) IMR90 cells were isolated using the acidic 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.