RNA-Seq: Characterizing short read sequencing for gene discovery and RNA-Seq analysis

Newsbot! · 01-17-2012, 06:50 AM

Syndicated from PubMed RSS Feeds

Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

Comp Biochem Physiol Part D Genomics Proteomics. 2011 Dec 29;

Authors: Gavery MR, Roberts SB

Abstract
Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genomes. However, there are limited examples that rely solely on ultra-short read sequencing technologies (e.g. Solexa, SOLiD) for transcript discovery and gene expression analysis (i.e. RNA-Seq). Here we use SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes. Gene enrichment analysis determined that in addition to biological processes predicted to be associated with anthropogenic influences (e.g. immune response), other processes play important roles including cell recognition and cell adhesion. To evaluate the effectiveness of restricting characterization solely to short read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold. This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms.

PMID: 22244882 [PubMed - as supplied by publisher]

More...

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
RNA-Seq: ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count da	Newsbot!	Literature Watch	0	11-18-2011 03:20 AM
RNA-Seq: deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.	Newsbot!	Literature Watch	0	06-01-2011 03:40 AM
RNA-Seq: Deep RNA sequencing analysis of readthrough gene fusions in human prostate a	Newsbot!	Literature Watch	0	01-26-2011 03:00 AM
RNA-Seq: Meiosis-specific gene discovery in plants: RNA-seq applied to isolated Arabi	Newsbot!	Literature Watch	0	12-21-2010 03:00 AM
RNA-Seq: Modeling non-uniformity in short-read rates in RNA-Seq data.	Newsbot!	Literature Watch	2	06-29-2010 02:47 PM

01-17-2012, 06:50 AM	#1
Newsbot! RSS Posting Maniac Join Date: Feb 2008 Posts: 1,443	RNA-Seq: Characterizing short read sequencing for gene discovery and RNA-Seq analysis Syndicated from PubMed RSS Feeds Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas. Comp Biochem Physiol Part D Genomics Proteomics. 2011 Dec 29; Authors: Gavery MR, Roberts SB Abstract Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genomes. However, there are limited examples that rely solely on ultra-short read sequencing technologies (e.g. Solexa, SOLiD) for transcript discovery and gene expression analysis (i.e. RNA-Seq). Here we use SOLiD sequencing to examine gene expression patterns in Pacific oyster (Crassostrea gigas) populations exposed to varying degrees of anthropogenic impact. Novel transcripts were identified and RNA-Seq analysis revealed several hundred differentially expressed genes. Gene enrichment analysis determined that in addition to biological processes predicted to be associated with anthropogenic influences (e.g. immune response), other processes play important roles including cell recognition and cell adhesion. To evaluate the effectiveness of restricting characterization solely to short read sequences, mapping and RNA-Seq analysis were also performed using publicly available transcriptome sequence data as a scaffold. This study demonstrates that ultra-short read sequencing technologies can effectively generate novel transcriptome information, identify differentially expressed genes, and will be important for examining environmental physiology of non-model organisms. PMID: 22244882 [PubMed - as supplied by publisher] More...