Differentiated somatic cells can be reprogrammed in induced pluripotent stem cells (iPSCs); a cell type with great potentials in regenerative medicine and in vitro disease modeling. In the pig, we have developed iPSCs, but proper culture conditions for maintaining pluripotency over time are still lacking. Hence, there is a need for a more fundamental dissection of the pluripotency apparatus in the pig as well as in cattle.
The aim of this study is to analyze RNA-seq data to increase the knowledge about biological pathways in porcine and bovine embryonic pluripotent cell populations exploiting the mouse data as proof of principle. In particular we studied cell populations from three different stages of pluripotency after fertilization: the inner cell mass, the epithelial epiblast and the gastrulating epiblast.
Reads quality was checked with FASTQC, then the reads were pre-processed using Prinseq and mapped with STAR aligner ending up with a minimum of 80% of uniquely mapped reads per sample. Post mapping quality control with Qualimap showed a minimum of 60% of reads mapped in the exonic regions per sample. Finally the expression levels were estimated using HTSeq.
Gene co-expression will be analyzed using a weighted network based method to identify highly co-expressed genes (module) and hub genes. Then modules with a potential role in pluripotency will be identified with an enrichment procedure and regulator genes identified with LemonTree algorithm. Finally differential wiring of the modules among species will be evaluated.
ACKNOWLEDGEMENTS: we thank for the financial support from the EU project PluriSys, HEALTH-2007-B-223485.