Comparative analysis of sequencing technologies for single-cell transcriptomics

• Main Authors: Kedar Nath Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Liang Wu, Naibo Yang, Bo Li, Yong Hou, Shiping Liu, Sarah A. Teichmann
• Format: Article
• Language: English
• Published: BMC 2019-04-01
• Series: Genome Biology
• Subjects: Single-cell RNA sequencing; Sequencing platforms; Benchmarking scRNA-seq; Illumina sequencing; BGISEQ-500
• Online Access: http://link.springer.com/article/10.1186/s13059-019-1676-5
• ISSN: 1474-760X

Abstract 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.