Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming III. Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming III

We collected triplicate samples at day 15 under serum condition, generated single cell suspensions and performed scRNA-Seq (10X Genomics). We also collected samples from a bulk population and performed bulk RNA-seq (Quantseq, Lexogen). Overall design: To determine the effect of GDF9 on reprogramming, we plated secondary MEFs at a concentration of 5,000 cells per well of a 24-well plate and added either recombinant mouse GDF9 daily from day 8 onward, or control. We tested different doses: 0.1 µg/ml, 0.5 µg/ml, and 1 µg/ml. We collected scRNA-seq profiles of ~50,000 cells at day 15 of iPSC induction under serum condition (10X Genomics). In addition, we collected bulk RNA-seq profiles (Quantseq, Lexogen).