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Nat Methods. 2014 Jan;11(1):51-4. doi: 10.1038/nmeth.2736. Epub 2013 Nov 24.

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.

Author information

1
Department of Genetics, Stanford University, Stanford, California, USA.
2
Department of Pathology, Stanford University, Stanford, California, USA.
3
McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada.
4
1] Department of Genetics, Stanford University, Stanford, California, USA. [2] Department of Pathology, Stanford University, Stanford, California, USA.

Abstract

We developed a targeted RNA sequencing method that couples microfluidics-based multiplex PCR and deep sequencing (mmPCR-seq) to uniformly and simultaneously amplify up to 960 loci in 48 samples independently of their gene expression levels and to accurately and cost-effectively measure allelic ratios even for low-quantity or low-quality RNA samples. We applied mmPCR-seq to RNA editing and allele-specific expression studies. mmPCR-seq complements RNA-seq for studying allelic variations in the transcriptome.

PMID:
24270603
PMCID:
PMC3877737
DOI:
10.1038/nmeth.2736
[Indexed for MEDLINE]
Free PMC Article
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