Fig. 1: Ascl1 and Ngn2 induce different alternative lineages.

a Schematic overview of the experimental design. b Scatter plot comparing gene expression at Day 6 between Ascl1 and Ngn2 Venus-positive cells with various neuronal subtype specific markers indicated in green. c, d Principal component analysis of time-resolved bulk RNAseq after Ascl1 (c) or Ngn2 (d). Each data point corresponds to the single time point replicate. Color intensity shows day post-induction. Shape corresponds the Mapt-Venus reporter upregulation. Arrows show the trajectory cells take after the Ascl1 (c) or Ngn2 induction (d). e, f Vulcano plot comparing gene expression between Venus-positive and negative populations at day 6 post-induction of Ascl1 (e) or Ngn2 (f). Red circles denote top significantly upregulated or downregulated genes as well as example genes marking in trophoblast (e) or NSC lineages (f). g Representative immunostained cells for a trophoblast marker CDX2 and a neuronal marker Map2 at day 6 post-induction of Ascl1 or Ngn2. Trophoblast markers were expressed only after Ascl1 induction, but not Ngn2. h Representative immunostained cells for an NSC marker PAX6 and a neuronal marker TUBB3 at day 6 post-induction of Ascl1 or Ngn2. NSC markers were expressed only after Ngn2 expression, but not Ascl1. i Scatter plot comparing gene expression changes between Ascl1 and Ngn2 at day 1 post-induction. Highlighted circles are example genes that are neuronal markers expressed in both (green), trophoblast Ascl1 specific markers (blue), NSC Ngn2 specific markers (yellow), pluripotency related genes (red). Source data are provided as a Source Data file.