3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

BMC Genomics
Yan W AsmannJean-Pierre A Kocher

Abstract

Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene expression (DGE). In this preliminary effort, we evaluated the 3' DGE approach using two reference RNA samples from the MicroArray Quality Control Consortium (MAQC). Using Brain RNA sample from multiple runs, we demonstrated that the transcript profiles from 3' DGE were highly reproducible between technical and biological replicates from libraries constructed by the same lab and even by different labs, and between two generations of Illumina's Genome Analyzers. Approximately 65% of all sequence reads mapped to mitochondrial genes, ribosomal RNAs, and canonical transcripts. The expression profiles of brain RNA and universal human reference RNA were compared which demonstrated that DGE was also highly quantitative with excellent correlation of differential expression with quantitative real-time PCR. Furthermore, one lane of 3' DGE sequencing, using the current sequencing chemistry and image processing software, had wider dynamic range for transcriptome profiling and was able to detect lower expressed genes which are normally ...Continue Reading

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Citations

Mar 11, 2011·Briefings in Functional Genomics·Nicole C RoyWarren C McNabb
Aug 19, 2011·Molecular Plant-microbe Interactions : MPMI·Wenwu YeYuanchao Wang
Aug 17, 2011·Genome Research·Lewis Z HongGregory S Barsh
Mar 29, 2012·Genome Research·Adnan DertiTomas Babak
Sep 14, 2010·Plant Physiology·Andrea L EvelandDavid Jackson
Nov 17, 2010·Respirology : Official Journal of the Asian Pacific Society of Respirology·Rebecca CullumPamela A Hoodless
Jul 11, 2013·BMC Bioinformatics·Jianqiang SunKoji Kadota
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Apr 6, 2012·Algorithms for Molecular Biology : AMB·Koji KadotaKentaro Shimizu
May 17, 2011·PloS One·Tal RazJohn F Thompson
Sep 18, 2014·Journal of Molecular Endocrinology·Petter VikmanNikolay Oskolkov
Nov 26, 2011·Journal of Invertebrate Pathology·Margot ParisLaurence Despres

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Datasets Mentioned

BETA
GSE5350

Methods Mentioned

BETA
PCR
RNA-Seq
or
quantitative

Software Mentioned

Ensembl
GA I
megaBLAST
Genome Analyzer
FireCrest
Illumina Genome Analyzer
Illumina Pipeline
GA
Bustard
MAQC

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