Extended Data Fig. 5: Further analyses of RNA-seq data from vitamin-C-deficient E13.5 female germ cells.
From: Maternal vitamin C regulates reprogramming of DNA methylation and germline development
a, Table of RNA-seq samples and number of germ cells per sample. Each sample represents germ cells from a single E13.5 female. b, Unsupervised hierarchical clustering of n = 6 biological replicates in each condition documents the overall separation between control and vitamin-C-deficient samples (columns) and relative gene expression (rows). 1CF1 denotes control litter 1, female embryo 1; 4VF2 denotes vitamin-C-deficient litter 4, female embryo 2. c, Scatterplot of differential gene expression in vitamin-C-deficient E13.5 female PGCs of genes differentially expressed in E13.5 Tet1−/− female PGCs8. Spearman’s rho statistic is used to estimate a rank-based measure of association. d, Expression of Dnmt and Tet genes in vitamin-C-deficient samples is similar to control samples. n = 6 biological replicates per condition. e, Heat map documenting the consistent expression of Tet and Dnmt genes across the six control and six vitamin-C-deficient samples. f, Expression of other genes belonging to families of enzymes with the potential to be vitamin C-sensitive (such as Kdm genes, collagen hydroxylases (P4h genes), prolyl hydroxylases (Lepre genes), HIF hydroxylases (Egln genes)). Lepre1 is also known as P3h1; Leprel1 is also known as P3h2; Leprel2 is also known as P3h3; and Leprel4 is also known as P3h4. None of these displays differential expression in vitamin-C-deficient female germ cells. n = 6 biological replicates per condition. Data are mean ± s.d. (d, f). Statistical significance assessed by two-tailed Student’s t-test (d, f). n.d., not determined.
