A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.

ABSTRACT:

Background

RNA-Seq exploits the rapid generation of gigabases of sequence data by Massively Parallel Nucleotide Sequencing, allowing for the mapping and digital quantification of whole transcriptomes. Whilst previous comparisons between RNA-Seq and microarrays have been performed at the level of gene expression, in this study we adopt a more fine-grained approach. Using RNA samples from a normal human breast epithelial cell line (MCF-10a) and a breast cancer cell line (MCF-7), we present a comprehensive comparison between RNA-Seq data generated on the Applied Biosystems SOLiD platform and data from Affymetrix Exon 1.0ST arrays. The use of Exon arrays makes it possible to assess the performance of RNA-Seq in two key areas: detection of expression at the granularity of individual exo

SUBMITTER: Bradford JR 

PROVIDER: S-EPMC2877694 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature