Warning: The NCBI web site requires JavaScript to function. more...

My NCBI Sign In

Result Filters

Nucleic Acids Res. 2009 Oct;37(18):e123. Epub 2009 Jul 20.

Transcriptome analysis by strand-specific sequencing of complementary DNA.

Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.

Source

Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestr. 73, 14195 Berlin, Germany.

Abstract

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.

PMID:: 19620212; [PubMed - indexed for MEDLINE]
PMCID:: PMC2764448

Free PMC Article

Images from this publication.See all images (4) Free text

Figure 2.

Figure 4.

Figure 1.

Figure 3.

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

Saccharomyces Genome Database

Supplemental Content

Icon for HighWire Press

Icon for PubMed Central

Save items

loading

Related citations in PubMed

A simple method for directional transcriptome sequencing using Illumina technology. [Nucleic Acids Res. 2009]
A simple method for directional transcriptome sequencing using Illumina technology.
Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T, Quail MA, He M, Assefa S, Bähler J, et al. Nucleic Acids Res. 2009 Dec; 37(22):e148.
The transcriptional landscape of the yeast genome defined by RNA sequencing. [Science. 2008]
The transcriptional landscape of the yeast genome defined by RNA sequencing.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. Science. 2008 Jun 6; 320(5881):1344-9. Epub 2008 May 1.
Strand-specific deep sequencing of the transcriptome. [Genome Res. 2010]
Strand-specific deep sequencing of the transcriptome.
Vivancos AP, Güell M, Dohm JC, Serrano L, Himmelbauer H. Genome Res. 2010 Jul; 20(7):989-99. Epub 2010 Jun 2.
Review [Transcriptomes for serial analysis of gene expression]. [J Soc Biol. 2002]
Review [Transcriptomes for serial analysis of gene expression].
Marti J, Piquemal D, Manchon L, Commes T. J Soc Biol. 2002; 196(4):303-7.
Review Tag-based approaches for transcriptome research and genome annotation. [Nat Methods. 2005]
Review Tag-based approaches for transcriptome research and genome annotation.
Harbers M, Carninci P. Nat Methods. 2005 Jul; 2(7):495-502.

See reviews... See all...

Cited by 29 PubMed Central articles

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. [Cell Rep. 2012]
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, et al. Cell Rep. 2012 Feb 23; 1(2):167-178.
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. [PLoS Genet. 2012]
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective.
DeVeale B, van der Kooy D, Babak T. PLoS Genet. 2012 Mar; 8(3):e1002600. Epub 2012 Mar 29.
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. [Database (Oxford). 2012]
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report.
Chan ET, Cherry JM. Database (Oxford). 2012; 2012:bar057. Epub 2012 Mar 20.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
SRA
Massively-parallel sequencing project data in the Short Read Archive (SRA) that are reported in the current articles.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Transcriptome analysis by strand-specific sequencing of complementary DNA.
Transcriptome analysis by strand-specific sequencing of complementary DNA.
Nucleic Acids Res. 2009 Oct ;37(18):e123. Epub 2009 Jul 20 .

PubMed
State variation in psychotropic medication use by foster care children with auti...
State variation in psychotropic medication use by foster care children with autism spectrum disorder.
Pediatrics. 2009 Aug ;124(2):e305-12. Epub 2009 Jul 20 .

PubMed
Cholesterol control beyond the clinic: New York City's trans fat restriction.
Cholesterol control beyond the clinic: New York City's trans fat restriction.
Ann Intern Med. 2009 Jul 21 ;151(2):129-34.

PubMed
The association of HIV susceptibility testing with survival among HIV-infected p...
The association of HIV susceptibility testing with survival among HIV-infected patients receiving antiretroviral therapy: a cohort study.
Ann Intern Med. 2009 Jul 21 ;151(2):73-84.

PubMed
Stereotactic radiosurgery in the management of brain metastases: an institutiona...
Stereotactic radiosurgery in the management of brain metastases: an institutional retrospective analysis of survival.
Int J Radiat Oncol Biol Phys. 2010 Apr ;76(5):1486-92. Epub 2009 Jul 18 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

You are here: NCBI > Literature > PubMed

Write to the Help Desk