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Fig. 4 | BMC Genomics

Fig. 4

From: The effect of methanol fixation on single-cell RNA sequencing data

Fig. 4

Molecular features of transcripts separating PC1 and PC2. (A) Plots of GC content and corresponding rank for the whole transcriptome. Highlighted events are those with top contributions in PC1 (left) and PC2 (right). GC contents of PC2 transcripts are generally higher compared with PC1 transcripts. (B) Plots of length and corresponding rank for the whole transcriptome. Highlighted events are those with top contributions in PC1 (left) and PC2 (right). Lengths of PC2 transcripts are generally higher compared with PC1 transcripts. (C) Comparisons of GC (top) and length (bottom) of transcripts with top contributions in PC1 and PC2. P-values show differences between live and fixed groups are both significant. Transcripts with top loading in PC2 are generally with longer lengths and higher GC contents compared with those in PC1. (D) Comparisons of relative abundances of transcripts with different lengths. We put a set of bars with increasing height at the bottom right corner to represent the transcript lengths. Highlighted bars represent the relative length of transcripts employed in that plot. As transcripts get longer, they gradually become more abundant in live cells than fixed cells. (E) Comparison of abundant transcript quantity in live and fixed cells. Groups separated by length. (F) Comparison of transcripts detection number. Groups are separated and arranged by increasing length. The number of transcript detection varies as length changes. Statistical significance p-values are determined by t-test and indicated with asterisks (ns P > 0.05, *P < 0.05, ****P < 0.0001)

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