Additional file 2 of Uncovering the role of the subcommissural organ in early brain development through transcriptomic analysis

Supplementary Material 2. Supplementary Fig. 2. Assessing inter- and intragroup variability. Analysis of the consistency and heterogeneity of transcriptomic data from SCO HH23, SCO HH30, and brain HH30. A) Principal component analysis plot: All samples were plotted along PC1 and PC2, capturing 62.75% and 24.2% of the variability, respectively, within the expression dataset. PCA of the normalized data was conducted using the median of ratio of DESeq2. B) Relative log expression plot: SCO samples exhibited a variation of less than ± 1, while brain data showed a variation of ± 2. C) List of primers used in the qPCR analysis. D) The normalized expression of transcripts for selected genes involved in axon guidance, differentiation, development, WNT-signaling, neuronal survival, and metabolism was validated by qPCR. E) The cycle threshold (ct) values for each gene were normalized to the GAPDH ct values. Four biological replicates were used, utilizing RNA from at least 15 animals. Error bars represent the standard deviation. Asterisks denote statistically significant differences (*p