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

  • Mane S
  • Evans C
  • Cooper K
 et al. 
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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

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Authors

  • S Mane

  • Clive Evans

  • K Cooper

  • O Crasta

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