Identifying genes differentially expressed in MDCK cells with scribble knock-down (scribKD)

Aim: To identify genes and pathways involved in elimination of scribKD cells by competition. Methods: We carried out mRNA sequencing of MDCK-II cells carrying a tetracycline-inducible scribble shRNA construct. We compared the transcriptomes of MDCK cells with scribble knock-down (scribKD+Tet) to that of control MDCK cells with wild-type scribble expression (scribKD-Tet) and to that of an isolate of scribKD cells that is resistant to cell competition (scribRES+Tet). The samples were obtained across at least two independent experiments. Each experiment contained at least two replicates per condition. mRNA profiles of three populations of MDCK-II cells were obtained by Illumina High-Throughput sequencing.