期刊
GENOME BIOLOGY
卷 20, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13059-019-1676-5
关键词
Single-cell RNA sequencing; Sequencing platforms; Benchmarking scRNA-seq; Illumina sequencing; BGISEQ-500
资金
- ERC [260507]
- Shenzhen Innovation Committee [JCYJ20170412153248372]
- Fundamental Central University research fund [x2swD2172910]
- P.R. China, MST Special Fund
- Wellcome Trust [108437/Z/15/Z, 105031/B/14/Z]
- SDU, Denmark
- VILLUM Fonden Young Investigator Award [00025397]
- Novo Nordisk [NNF18OC0052874]
- Chinese Ministry of Science and Technology
- Wellcome Trust [108437/Z/15/Z, 105031/B/14/Z] Funding Source: Wellcome Trust
- European Research Council (ERC) [260507] Funding Source: European Research Council (ERC)
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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