Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing.

ABSTRACT:

Background

Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC) reference RNA samples using Roche's 454 Genome Sequencer FLX.

Results

We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values

SUBMITTER: Mane SP 

PROVIDER: S-EPMC2707382 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature