In that seminal study, researchers manually picked single cells under a microscope, prepared an RNA-Seq library from each cell in the well of a standard microplate, and performed next generation sequencing (NGS) on the now-obsolete ABI ® SOLiD™ platform. Single-cell sequencing has changed markedly since its first publication in 2009 1.
Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Zhang L., Yu X., Zheng L., Zhang Y., Li Y., Fang Q., et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Pollen A.A., Nowakowski T.J., Shuga J., Wang X., Leyrat A.A., Lui J.H., et al. mRNA-seq whole-transcriptome analysis of a single cell. Tang F., Barbacioru C., Wang Y., Nordman E., Lee C., Xu N., et al. Our study promotes better understanding of these two platforms and offers the basis for an informed choice of these widely used technologies.ġ0X Bulk RNA-seq Comparison Single-cell RNA sequencing Smart-seq2.Ĭopyright © 2021 The Authors. In addition, each platform detected distinct groups of differentially expressed genes between cell clusters, indicating the different characteristics of these technologies. However, 10X-data can detect rare cell types given its ability to cover a large number of cells. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. Approximately 10%-30% of all detected transcripts by both platforms were from non-coding genes, with long non-coding RNAs (lncRNAs) accounting for a higher proportion in 10X. For 10X-based data, we observed higher noise for mRNAs with low expression levels. The composite of Smart-seq2 data also resembled bulk RNA-seq data more.
Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. Here, by directly comparing the scRNA-seq data generated by these two platforms from the same samples of CD45 - cells, we systematically evaluated their features using a wide spectrum of analyses. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Single-cell RNA sequencing (scRNA-seq) is generally used for profiling transcriptome of individual cells.
0 kommentar(er)
