Comparative analysis of sequencing technologies for single-cell transcriptomics
| Autor: | Kedar Nath Natarajan, Sarah A. Teichmann, Zhichao Miao, Shishang Qin, J. Xie, Liang Wu, Shiping Liu, Miaomiao Jiang, Zhikun Zhao, Hongpo Zhou, Chunqing Wang, Naibo Yang, Bo Li, Xiaoyun Huang, Yong Hou |
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| Přispěvatelé: | Natarajan, Kedar Nath [0000-0002-9264-1280], Apollo - University of Cambridge Repository |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
lcsh:QH426-470
Single cell transcriptomics Library preparation BGISEQ-500 Sequencing platforms genetic processes Short Report Computational biology Biology Single-cell RNA sequencing 03 medical and health sciences Mice 0302 clinical medicine Single-cell analysis Animals Humans natural sciences lcsh:QH301-705.5 Illumina dye sequencing 030304 developmental biology Benchmarking scRNA-seq 0303 health sciences Sequence Analysis RNA Gene Expression Profiling Illumina sequencing Gene expression profiling lcsh:Genetics lcsh:Biology (General) Benchmark (computing) Single-Cell Analysis K562 Cells 030217 neurology & neurosurgery |
| Zdroj: | Natarajan, K N, 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, S A 2019, ' Comparative analysis of sequencing technologies for single-cell transcriptomics ', Genome Biology, vol. 20, 70 . https://doi.org/10.1186/s13059-019-1676-5 Genome Biology Genome Biology, Vol 20, Iss 1, Pp 1-8 (2019) |
| Popis: | 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. Electronic supplementary material The online version of this article (10.1186/s13059-019-1676-5) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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