Fig. 2
From: The effect of methanol fixation on single-cell RNA sequencing data
Principal component analysis of data generated from two cell lines. (A) PCA visualizing different treatments and annotations. The first column visualizes PC1 and PC2. The third column visualizes using PC1 and PC3. The second column visualizes PC1 and PC2 after cell cycle effect removal. Cells in the same row are annotated using the same terms. Cell type confers the greatest degree of variance in the dataset as shown by the first PC, followed by cycle and fixation effect. Key biological differences between cell types are not obscured by the fixation effect. (B) PCA of the individual cell line. Both PC1s are separated by cell cycle effect, while PC2s are separated by the fixation treatment. (C) Gene ontology terms of 500 genes with the top contribution in separating the first and second PCs in both cell lines. We further validated the smear pattern in Fig. 2 A was caused by cell cycle effect and the separation between live and fixed cells is not caused by biological reasons