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. 2021 Nov 25;50(4):e19. doi: 10.1093/nar/gkab1129

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Identification of differential gene and isoform expression. (A, B) Principal component analysis (PCA) of sequin (A) and SH-SY5Y (B) gene and isoform expression between undifferentiated and differentiated SH-SY5Y cells. All plots show the first two principal components. SH-SY5Y shows endogenous expression only. Sequins were added to undifferentiated (Mix A) and differentiated (Mix B) SH-SY5Y RNA and plots reflect measured abundance differences between the sequin mixes. (C, D) Quantification of fold changes between Mix A and Mix B sequin genes (C) and isoforms (D). Comparison of known fold changes in abundance with measured fold changes from sequencing. Sequins with significant differential expression in blue, not significant in grey. Trend line shows slope from linear regression. Shaded grey area shows 95% confidence interval for regression slope. Correlation (r) is spearman correlation. (E) Volcano plot of differential isoform expression between undifferentiated and differentiated SH-SY5Y cells. An adjusted P-value <0.05 (from DESeq2) was considered significant for differential expression. FC = fold change. (F) Gene ontology (GO) terms most associated with differentially expressed genes upregulated during SH-SY5Y differentiation. P-values adjusted using Bonferroni correction for multiple testing.