Analysis of differential gene expression in Regorafenib resistant human HCC cells either expressing or lacking Axl

Human HCC cell line SNU449 and SNU449-Axl-KO were cultured in increasing concentrations of Regorafenib (Rego) to generate resistance. Treatment naive cells (SNU449-ctrl and SNU449-Axl-KO-ctrl) and resistant ones (SNU449-Rego and SNU449-Axl-KO-Rego) were sent for RNA-seq. Overall design: Differential gene expression analysis was performed based on RNA-seq data of SNU449-ctrl, SNU449-Axl-KO-ctrl, SNU449-Rego and SNU449-Axl-KO-Rego. Analysis was done in technical triplicates for each cell line. SNU449_wt_parental_r1 to r3 = SNU449-ctrl as there is no Axl KO and no resistance induced. Three replicates for sequencing (r1-r3). SNU449_wt_plusRego_r1 to r3 = SNU449-Rego. No Axl KO but Regorafenib resistance. Three replicates for sequencing (r1-r3). SNU449_AxlKO_parental_r1 to r3 = SNU449-Axl-KO-ctrl as there is a Axl KO but no resistance induced. Three replicates for sequencing (r1-r3) SNU449_AxlKO_plusRego_r1 to r3 = SNU449-Axl-KO-Rego as there is a Axl KO and Regorafenib resistance.. Three replicates for sequencing (r1-r3)