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Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.

ABSTRACT: Targeted RNA sequencing (RNA-seq) aims to focus coverage on areas of interest that are inadequately sampled in standard RNA-seq experiments. Here we present multiplexed primer extension sequencing (MPE-seq), an approach for targeted RNA-seq that uses complex pools of reverse-transcription primers to enable sequencing enrichment at user-selected locations across the genome. We targeted hundreds to thousands of pre-mRNA splice junctions and obtained high-precision detection of splice isoforms, including rare pre-mRNA splicing intermediates.

SUBMITTER: Xu H

PROVIDER: S-EPMC6414223 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.

Xu Hansen H Fair Benjamin J BJ Dwyer Zachary W ZW Gildea Michael M Pleiss Jeffrey A JA

Nature methods 20181220 1

Targeted RNA sequencing (RNA-seq) aims to focus coverage on areas of interest that are inadequately sampled in standard RNA-seq experiments. Here we present multiplexed primer extension sequencing (MPE-seq), an approach for targeted RNA-seq that uses complex pools of reverse-transcription primers to enable sequencing enrichment at user-selected locations across the genome. We targeted hundreds to thousands of pre-mRNA splice junctions and obtained high-precision detection of splice isoforms, inc ...[more]

PMID: 30573814

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Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates.

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