Bulk RNA-seq of PSCs and induced PSM cells from six different mammalian species
In this study, we performed bulk RNA-seq of pluripotent stem cells (PSCs) and induced pre-somitic mesoderm (PSM) cells of six different mammalian species. The species studied are: mouse (Mus musculus), marmoset (Callithrix jacchus), rabbit (Oryctolagus cuniculus), human (Homo sapiens), cattle (Bos taurus) and southern white rhinoceros (Ceratotherium simum). We used mouse ESCs, marmoset iPSCs, rabbit ESCs, human iPSCs, bovine ESCs and rhinoceros ESCs to induce PSM-like cells from these species following protocols already described. PSC samples were extracted under maintenance conditions. PSM samples were extracted on the day when the differentiation efficiency was higher based on the percentage of cells expressing the PSM marker TBX6. We used identical culture conditions when extracting the induced PSM cells to minimize the effect of external factors on our results. Two replicates per each cell type and species were collected for a total of 24 samples. We compared the expression levels of more than 10,000 orthologous protein-coding genes across the six species. With this, we determined that the species-specific segmentation clock periods might be derived from species-specific gene expression profiles controlling basic biological processes.