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Genome Biol. 2015 Sep 30;16:204. doi: 10.1186/s13059-015-0777-z.

Determining exon connectivity in complex mRNAs by nanopore sequencing.

Author information

1
Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
2
Present Address: The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA.
3
Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA. graveley@uchc.edu.

Abstract

Short-read high-throughput RNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maximum read length. Here, we use the Oxford Nanopore MinION sequencer to identify 7,899 'full-length' isoforms expressed from four Drosophila genes, Dscam1, MRP, Mhc, and Rdl. These results demonstrate that nanopore sequencing can be used to deconvolute individual isoforms and that it has the potential to be a powerful method for comprehensive transcriptome characterization.

PMID:
26420219
PMCID:
PMC4588896
DOI:
10.1186/s13059-015-0777-z
[Indexed for MEDLINE]
Free PMC Article

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