Comparative analysis of sequencing technologies for single-cell transcriptomics.
Published version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Natarajan, Kedar Nath https://orcid.org/0000-0002-9264-1280
Miao, Zhichao
Jiang, Miaomiao
Huang, Xiaoyun
Zhou, Hongpo
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.
Description
Keywords
BGISEQ-500, Benchmarking scRNA-seq, Illumina sequencing, Sequencing platforms, Single-cell RNA sequencing, Animals, Gene Expression Profiling, Humans, K562 Cells, Mice, Sequence Analysis, RNA, Single-Cell Analysis
Journal Title
Genome Biol
Conference Name
Journal ISSN
1474-7596
1474-760X
1474-760X
Volume Title
20
Publisher
Springer Science and Business Media LLC