Transcriptome analysis by strand-specific sequencing of complementary DNA | Zendy

Dmitri Parkhomchuk | Zendy; Tatiana Borodina | Zendy; Vyacheslav Amstislavskiy | Zendy; Maria Banaru | Zendy; Linda Hallen | Zendy; Sylvia Krobitsch | Zendy; Hans Lehrach | Zendy; А. В. Солдатов | Zendy

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Transcriptome analysis by strand-specific sequencing of complementary DNA

Author(s) -

Dmitri Parkhomchuk,

Tatiana Borodina,

Vyacheslav Amstislavskiy,

Maria Banaru,

Linda Hallen,

Sylvia Krobitsch,

Hans Lehrach,

А. В. Солдатов

Publication year - 2009

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkp596

Subject(s) - biology , transcriptome , gene , genetics , computational biology , dna sequencing , transcription (linguistics) , dna , complementary dna , rna seq , saccharomyces cerevisiae , rna , gene expression , linguistics , philosophy

High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online

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