Extended Data Fig. 9: Hs-HARE5-dependent transcriptome supports neurogenic transition across cortical development.

a, Experimental paradigm for sample collection for Bulk-RNA sequencing of control (n = 3) and HARE5^Hs/Hs (n = 3) cortices for each stage, E12.5 and E14.5, from 5 litters. b, Scatter plot shows the correlation of log2Fold Change values for all transcripts differentially expressed from E12.5 to E14.5 of control and HARE5^Hs/Hs cortex. Colored dots represent significant changes in differential expression in indicated genotypes. The gene Pakap was omitted from the plot for clarity as it had log2Fold change <-10 in both genotypes. c, Criteria used to identify statistically significant gene expression in HARE5^Hs/Hs cortices from E12.5 to E14.5. d, Proportional Venn diagram of the genes expressed in controls, HARE5^Hs/Hs cortices, and their overlap. The diagram was drawn using BioVenn. e,f, Gene Ontology analysis (biological process) showing all statistically significant enriched categories from E12.5 to 14.5 in HARE5^Hs/Hs cortices for upregulated transcripts (e) and downregulated genes (f). The x-axis indicates the fold change in expression. g, Gene Ontology analysis showing all statistically significant enriched categories for upregulated (top) and downregulated (bottom) transcripts from E12.5 to 14.5 in control cortices. The x-axis indicates the fold change in expression. DE genes are listed in Supplementary Table 2. Statistics for RNA-seq differential gene expression (b,c) were performed using the DE-seq2 package (see Supplemental Table 2 for Padj values).