Fig. 2: SNIP1 suppresses genes involved in apoptosis and signal transduction and promotes genes for brain development.

a Schematic of the brain NPC collection. b Volcano plot and the number of differentially expressed genes between the control and Snip1^Nes-KO NPCs. The table shows the number of genes that passed the cutoff of FDR < 0.05. FDR was calculated by the Benjamini & Hochberg method. P values were calculated by two-sided Voom-limma t test. c, i Bubble plots of the enriched gene sets in upregulated genes and downregulated genes in Snip1^Nes-KO vs. control NPCs. Differentially expressed genes were first ranked by their fold-change, p-value, and expression level before Gene Set Enrichment Analysis (GSEA) was performed. P-values were calculated by a right-sided permutation test with FDR adjustment. d, e Representative GSEA of upregulated genes in Snip1^Nes-KO vs. control NPCs. Upregulated genes were enriched in gene sets related to both intrinsic and extrinsic apoptosis. Differentially expressed genes were first ranked by their fold-change and p-value before GSEA was performed. f IF of cleaved caspase 9 (CC9) overlayed with SOX2 in sagittal cryosections of the E13.5 brain. Bar, 50 μm. g Schematic of transduction with mCherry-Cre lentivirus and treatment with inhibitors in Snip1[+/+] and Snip1[flox/flox] NPCs. h The percentage of cells with active caspase 3 quantified by FACS. Caspase 9 inhibitor (Z-LEHD-FMK) was added at different concentrations along with mCherry-Cre lentivirus. The percentage of FAM-FLICA (active caspase 3)-positive population (out of total population) is shown. N = 12 for DMSO control and n = 6 for the rest of the sample. Data are presented as mean ± SEM, and two-way ANOVA was used for statistical analysis. The gating strategy and representative FACS plots are shown in Supplementary Information (Supplementary Fig. 4e, Supplementary Fig 14a). Source data are provided in a Source Data file (c, h, i).