Transcriptomic analysis of senescent cells upon PTBP1 knockdown.

IMR90 ER:RAS cells were stably transduced with either an empty vector or 2 deconvoluted shRNAs targeting PTBP1. Following selection with puromycin, the cells were treated with 4OHT to induce senescence. 6 days later the cells were collected for total mRNA analysis. PTBP1 is a regulator of alternative splicing. Our previous experiments had shown that PTBP1 depletion inhibits the expression of pro-inflammatory genes without affecting other senescence-associated phenotypes. By performing RNA-seq we confirmed those observations at a global level and analysed how PTBP1 knockdown alters alternative splicing as a potential mechanism of action. Overall design: 4 conditions were examined: proliferating cells (Vector), senescent cells (Vector + 4OHT), senescent cells expresssing an shRNA targeting PTBP1 (shPTBP1_53 + 4OHT) and senescent cells expressing a different shRNA targeting PTBP1 (shPTBP1_86 + 4OHT).