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Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

本站小编 Free考研考试/2022-01-03

Single-cell RNA sequencing (scRNA-seq) is generally used for profiling transcriptome of individual cells. 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. 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. 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. The composite of Smart-seq2 data also resembled bulk RNA-seq data more. For 10X-based data, we observed higher noise for mRNAs with low 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. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected distinct groups of differentially expressed genes between cell clusters, indicating the different characteristics of these technologies. Our study promotes better understanding of these two platforms and offers the basis for an informed choice of these widely used technologies.
单细胞RNA测序(scRNA-seq)通常用于描述单个细胞的转录组。基于液滴的10X和基于细胞板的Smart-seq2是两种常用的scRNA-seq建库体系,但目前只有极少数的研究系统的比较了这两种体系的优势和局限性。本研究用这两种体系对同样的取自肿瘤的CD45-细胞进行了单细胞测序,并对测序数据进行了系统的评估。我们发现在单个细胞内Smart-seq2可以发现更多的基因,特别是低表达丰度的基因,Smart-seq2的数据也特别适合分析转录本的选择性剪接,但捕获的线粒体基因的比例更高。Smart-seq2数据与传统的高通量RNA-seq数据更为相似。而10x数据则在低表达的mRNA中观察到了更高的噪声。在两种体系的数据中都观察到了约10%?30%的转录本来自非编码基因,尤其是在10X数据中所占比例更高高。10x数据展示出更为严重的漏检率,特别是对低表达的基因。但是由于10x数据能够同时获得大量细胞,因此可以检测到罕见的细胞类型。此外,这两种体系检测到了相同细胞亚群之间不同的差异表达基因,说明了不同体系的各自特性。本文有助于研究者更好地理解这两种不同技术,并为研究者选择单细胞建库体系提供了依据。





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