Gene expression profiling using RNA-sequencing in mouse embryonic stem cells under control conditions or Phf5a knockdown

Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed gene expression profiling using RNA-sequncing in mouse ESCs under conditions of self-renewal, Phf5a knockdown and Paf1 knockdown. These results revealed that Phf5a and Paf1 regulate similar gene expression signatures in mouse ESCs. RNA was extracted from 10 million self-renewing, Phf5a knockdown or Paf1 knockdown treated ESCs using Trizol extraction (Invitrogen) according to the manufacturer’s protocol following Poly-A selection which was then used for library preparation. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Gene expression analysis was performed for matched shControl versus shPhf5a or shPaf1 knockdown in each biological replicate.