Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

The hippocampal expression profiles of wild-type mice and mice transgenic for deltaC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray platforms. With Illumina's digital gene expression assay, we obtained approximately 2.4 million sequence tags per sample, their abundance spanning four orders of magnitude. Results were highly reproducible, even across laboratories. With a dedicated Bayesian model, we found differential expression of 3179 transcripts with an estimated false-discovery rate of 8.5%. This is a much higher figure than found for microarrays. The overlap in differentially expressed transcripts found with deep sequencing and…

• NO
  Nederlandse Organisatie voor Wetenschappelijk Onderzoek
• LU
  Leids Universitair Medisch Centrum