Gene expression difference in cells expressing high and low FoxA2-Venus protein levels from mouse neural tube organoids.

We describe the transcriptomic differences in FoxA2-Venus high and low cell populations in neural tube organoids. Organoids were grown via clonal growth from R1 mouse ES cells of FoxA2-Venus genotype seeded in Matrigel and cultured in N2B27 medium at 37C, 5% CO2 as described (Meinhardt et al. Stem Cell Reports 2014, Ishihara et al. Methods in Mol. Bio. 2017). At Day 2 (=48 hrs post seeding), organoids were treated with or without 250 nM all trans retinoic acid. Organoids were extracted from the Matrigel at 66 hrs post Day 2 and FACS sorted based on high and low fluorescence signal using a GFP filter set, yielding the categories GFP+ and GFP-. Three biological replicates were prepared for each cell population, yielding 9 independent samples for RNA extraction.