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PMID: 24270603 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.

Nature methods ·Vol. 11 ·No. 1 ·2014-01-00 ·Pages 51-4

Zhang R, Li X, Ramaswami G, Smith KS, Turecki G, Montgomery SB, Li JB

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.

MeSH Terms
Alleles Brain/metabolism,pathology DNA Barcoding, Taxonomic DNA, Complementary/metabolism Gene Expression Profiling Genotype High-Throughput Nucleotide Sequencing/methods Humans Multiplex Polymerase Chain Reaction/methods RNA/analysis RNA Editing Reproducibility of Results Reverse Transcriptase Polymerase Chain Reaction/economics,methods Sequence Analysis, RNA/economics,methods Transcriptome
Chemicals
DNA, Complementary RNA
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Zhang Rui
Department of Genetics, Stanford University, Stanford, California, USA.
Li Xin
Department of Pathology, Stanford University, Stanford, California, USA.
Ramaswami Gokul
Department of Genetics, Stanford University, Stanford, California, USA.
Smith Kevin S
Department of Pathology, Stanford University, Stanford, California, USA.
Turecki Gustavo
McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada.
Montgomery Stephen B
1] Department of Genetics, Stanford University, Stanford, California, USA. [2] Department of Pathology, Stanford University, Stanford, California, USA.
Li Jin Billy ORCID
Department of Genetics, Stanford University, Stanford, California, USA.
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.2736
Published
2014-01-00
Epub
2013-00-24
Pages
51-4
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC3877737
Subset
IM
Grants
NIGMS NIH HHS · R01 GM102484 · United States
NHGRI NIH HHS · T32 HG000044 · United States
NIGMS NIH HHS · GM102484 · United States
Databases
SRA
SRP029341
External Links
PubMed source DOI: 10.1038/nmeth.2736 PMC Full Text View journal details
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