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Nat Methods. 2014 Jan;11(1):41-6. doi: 10.1038/nmeth.2694. Epub 2013 Oct 20.

Quantitative assessment of single-cell RNA-sequencing methods.

Author information

1
Department of Bioengineering, Stanford University, Stanford, California, USA.
2
1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2].
3
1] Department of Medicine, Division of Oncology, Stanford University Medical Center, Stanford, California, USA. [2] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University Medical Center, Stanford, California, USA. [3] The Ludwig Cancer Center, Stanford University Medical Center, Stanford, California, USA.
4
Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University Medical Center, Stanford, California, USA.
5
1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2] Howard Hughes Medical Institute, Stanford, California, USA.
6
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University Medical Center, Stanford, California, USA.
7
1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2] Howard Hughes Medical Institute, Stanford, California, USA. [3] Department of Applied Physics, Stanford University, Stanford, California, USA.

Abstract

Interest in single-cell whole-transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. We compared commercially available single-cell RNA amplification methods with both microliter and nanoliter volumes, using sequence from bulk total RNA and multiplexed quantitative PCR as benchmarks to systematically evaluate the sensitivity and accuracy of various single-cell RNA-seq approaches. We show that single-cell RNA-seq can be used to perform accurate quantitative transcriptome measurement in individual cells with a relatively small number of sequencing reads and that sequencing large numbers of single cells can recapitulate bulk transcriptome complexity.

PMID:
24141493
PMCID:
PMC4022966
DOI:
10.1038/nmeth.2694
[Indexed for MEDLINE]
Free PMC Article
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