Fig. 3: Ncf1 represses NSC DNA repair pathways in an Igfbp2-dependent manner.

NSCs prepared from 4 WT (A, B, C, and D) and 4 Ncf1^–/– mice were treated with vehicle (1, 2, 3, and 4) or Igfbp2 (1I, 2I, 3I, and 4I) 48 h after plating. Vehicle- and Igfbp2-treated Ncf1^–/– groups are matched for NSC preparation by the number with “I” indicating Igfbp2-treatment. After additional 48 h, total RNA was collected from all groups and ribosome-depleted RNAseq was performed. a–c Heat maps represent clustering based on Euclidean distance of all genes that were significantly differentially expressed between any of the three groups (WT, Ncf1^–/–, and Igfbp2-treated Ncf1^–/– NSCs) (a), WT and Ncf1^–/– (b), and WT and Ncf1^–/– for which expression was restored towards WT levels after treatment with Igfbp2 (c). Statistical analysis of changes in gene expression used Benjamini–Hochberg FDR corrected one-way ANOVAs (a) and Tukey’s post hoc tests (b, c). d Ingenuity Pathway Analysis (IPA) performed on the gene sets in (c) using the absolute fold change for Ncf1^–/– vs. WT and Ncf1^–/– + Igfbp2 vs. Ncf1^–/– revealed the top pathway: Role of Brca1 in DNA Damage Response (P = 0.0010 and P = 0.0017, respectively) (Supplementary Data 3b). Subset of genes in the Brca1 pathway that are expressed differentially in each of the experimental groups. TPM: transcript per million. Benjamini–Hochberg corrected One-way ANOVA followed by Tukey’s multiple comparison post hoc test, N = 4 donors. Source data are provided as a Source data file.