RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of the Illumina sequencing (formerly Solexa sequencing) platform to study mRNA expression levels. Our goals were to estimate technical variance associated with Illumina sequencing in this context and to compare its ability to identify differentially expressed genes with existing array technologies. To do so, we estimated gene expression differences between liver and kidney RNA samples using multiple sequencing replicates, and compared the sequencing data to results obtained from…

• AP
  Alfred P. Sloan Foundation
• YU
  Yale University
• UO
  University of Chicago
• NI
  National Institutes of Health

  Awards: HG002585, NS051869, GM077959