Step-wise differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells (mESCs) using developmental logic [bulk RNA-seq]

We directed mESCs towards the neuromesodermal progenitor state (NMPs) that contribute to the spinal cord cells in the embryo. We then tested if ESC-derived NMPs can be directed to generate diverse sensory neuronal subtypes by testing different combinations of growth factors RA and BMP4 which are crucial for providing patterning information during spinal cord development. By bulk-RNA seq analysis of the entire timeline of the mESC differentiation under various conditions, we identified differentiation trajectories that lead to sensory neurons or completely different cardiac cell types under RA/+BMP4 conditions. We also characterized the gene expression changes that occur when cells transition from different states while differentiating into sensory neurons and identified Wnt signaling being a regulator of proliferation working directly downstream of BMP4 signaling in the mESC cultures. Overall design: 3- replicate samples were collected at each time points between day 0 and day 9 under different conditions. Total 45 samples were collected from 3-independent differentiations.