Comparative analysis of sequencing technologies for single-cell transcriptomics

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

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Original languageEnglish
Article number70
JournalGenome Biology
Volume20
Number of pages8
ISSN1474-7596
DOIs
Publication statusPublished - 2019

Fingerprint

Small Cytoplasmic RNA
transcriptomics
Libraries
RNA
DNA libraries
Benchmarking
cell lines
cells
resource
gene expression
Complementary DNA
Cell Line
sampling
analysis
library
protocol

Keywords

  • Benchmarking scRNA-seq
  • BGISEQ-500
  • Illumina sequencing
  • Sequencing platforms
  • Single-cell RNA sequencing

Cite this

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. / Comparative analysis of sequencing technologies for single-cell transcriptomics. In: Genome Biology. 2019 ; Vol. 20.
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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.",
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author = "Natarajan, {Kedar Nath} and Zhichao Miao and Miaomiao Jiang and Xiaoyun Huang and Hongpo Zhou and Jiarui Xie and Chunqing Wang and Shishang Qin and Zhikun Zhao and Liang Wu and Naibo Yang and Bo Li and Yong Hou and Shiping Liu and Teichmann, {Sarah A.}",
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doi = "10.1186/s13059-019-1676-5",
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Natarajan, KN, Miao, Z, Jiang, M, Huang, X, Zhou, H, Xie, J, Wang, C, Qin, S, Zhao, Z, Wu, L, Yang, N, Li, B, Hou, Y, Liu, S & Teichmann, SA 2019, 'Comparative analysis of sequencing technologies for single-cell transcriptomics', Genome Biology, vol. 20, 70. https://doi.org/10.1186/s13059-019-1676-5

Comparative analysis of sequencing technologies for single-cell transcriptomics. / 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.

In: Genome Biology, Vol. 20, 70, 2019.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - Comparative analysis of sequencing technologies for single-cell transcriptomics

AU - Natarajan, Kedar Nath

AU - Miao, Zhichao

AU - Jiang, Miaomiao

AU - Huang, Xiaoyun

AU - Zhou, Hongpo

AU - Xie, Jiarui

AU - Wang, Chunqing

AU - Qin, Shishang

AU - Zhao, Zhikun

AU - Wu, Liang

AU - Yang, Naibo

AU - Li, Bo

AU - Hou, Yong

AU - Liu, Shiping

AU - Teichmann, Sarah A.

PY - 2019

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N2 - 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.

AB - 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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KW - Sequencing platforms

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