Comparative analysis of sequencing technologies for single-cell transcriptomics
2019
Natarajan, Kedar Nath | Miao, Zhichao | Jiang, Miaomiao | Huang, Xiaoyun | Zhou, Hongpo | Xie, Jiarui | Wang, Chunqing | Qin, Shishang | Zhao, Zhikun | Wu, Liang | Yang, Naibo | Li, Bo | Hou, Yong | Liu, Shiping | Teichmann, Sarah A.
Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins. We sequence these libraries on both platforms using single- and paired-end reads. The platforms have comparable sensitivity and accuracy in terms of quantification of gene expression, and low technical variability. Our study provides a standardized scRNA-seq resource to benchmark new scRNA-seq library preparation protocols and sequencing platforms.
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