Fig. 4: Genome-wide gene expression analysis of Ring1B-null NPCs derived from the ventral telencephalon.

a Genome-wide gene expression in NPCs isolated from the GE of control or Ring1B KO mice at E11 was analyzed by Quartz-seq analysis. A total of three samples prepared from one, one, or two embryos was analyzed for each genotype. b, c Genes whose expression was upregulated (b) or downregulated (c) in NPCs of Ring1B KO mice were defined as those whose Ring1B KO/control or control/Ring1B KO fold change, respectively, was ≥1.5 on average and ≥1.2 in each experiment, with a false discovery rate (FDR) of <0.15 (left panels). The genes with the 10 lowest p values (determined with edgeR) in each category are also listed (right panels). d, e Enriched pathways among upregulated genes (d) and downregulated genes (e) were determined by KEGG pathway analysis. p values were determined with DAVID Bioinformatic Resources. For the full list of differentially expressed genes and enriched pathways, see Supplementary Data 1. f RT-qPCR analysis of the relative abundance of Bmp4 and Id1 mRNAs (normalized by the amount of Actb mRNA) in NPCs of control or Ring1B KO mice at E11. Data are means ± s.d., averaged values for n = 4 l (the number and individual values of each littermate are provided in Source Data File), two-tailed Student’s paired t test. g RT-qPCR analysis of the relative abundance of Wnt7b, Wnt8b, and Axin2 mRNAs (normalized by the amount of Actb mRNA) in NPCs of control or Ring1B KO mice at E11. Data are means ± s.d., n = 13–16 (15 for Wnt7b, 13 for Wnt8b, 16 for Axin2) control and n = 5 Ring1B KO mice from three litters, two-tailed Student’s unpaired t test. Source data are provided as a Source Data file.