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.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Alleles
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Brain / metabolism
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Brain / pathology
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DNA Barcoding, Taxonomic
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DNA, Complementary / metabolism
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Gene Expression Profiling
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Genotype
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High-Throughput Nucleotide Sequencing / methods*
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Humans
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Multiplex Polymerase Chain Reaction / methods*
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RNA / analysis*
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RNA Editing
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Reproducibility of Results
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Reverse Transcriptase Polymerase Chain Reaction / economics
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Reverse Transcriptase Polymerase Chain Reaction / methods
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Sequence Analysis, RNA / economics
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Sequence Analysis, RNA / methods*
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Transcriptome