Figure 4
From: Single-cell DNA and RNA sequencing of circulating tumor cells
Performance of NGS in WTA sample. (a) Numbers of sequenced reads from transcripts in WTA samples by each method. The number of sequenced reads by method Z (MDA-based) was much lower than those of the other methods (PCR-based). However, most expressed genes in single cell can be detected with 0.5 × 106 reads and almost all samples yielded over 0.5 × 106 reads from transcripts. (b) Numbers of expressed genes in WTA samples by each method. We defined transcripts with over 100 sequenced reads as expressed genes. The number of expressed genes was comparable between each sample, and method X (PCR-based) amplified higher number of expressed genes compared to the other methods. (c) Scatter plot of normalized read counts of expressed genes in the bulk sample and WTA samples by each method. Sequenced reads from transcripts were normalized by DESeq and correlation analysis of the gene expression patterns between the bulk sample and WTA samples was performed by Spearman’s test. The samples by method X (PCR-based) correlated well with the bulk sample compared to the other methods (R = 0.70). (d) Gene expression patterns in the bulk sample and WTA samples by each method. According to scatter plot, the gene expression patterns of the samples by method X resembled those of the bulk sample. In contrast, samples by method Z (MDA-based) showed non-specific gene expression patterns.
