Transcriptome profiling of rattus norvegicus embryonic stem cells by RNA-sequencing
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Embryonic Stem Cells (ESCs) are a critical tool for producing targeted knockout animals and understanding development. ESCs were successfully isolated from rats in 2008 and have been used in producing several targeted knockout animal models. To date, little characterization of rat ESCs (rESCs) has been done. In order to establish a rESC transcriptome, RNA-Seq was done on mRNA from the rESC cell line DAc8, the first male germline competent rat ESC line to be described and the first to be used to generate a knockout rat model. RNA-Seq was chosen as it is currently the most sensitive transcriptome analysis method. In the studies described here, the genes expressed in rat ESCs were identified, and a subset of the undescribed isoforms and unannotated rat genes revealed by this analysis were confirmed by RT-PCR analysis. Importantly, the rESC data allowed comparison with previously reported data for mouse and human ESCs to begin to understand the similarities and differences of the transcriptomes of ESCs from different mammalian species.
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M.S.