A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.

ABSTRACT:

Background

The past decade has seen an abundance of transcriptional profiling studies of preclinical models of persistent pain, predominantly employing microarray technology. In this study we directly compare exon microarrays to RNA-seq and investigate the ability of both platforms to detect differentially expressed genes following nerve injury using the L5 spinal nerve transection model of neuropathic pain. We also investigate the effects of increasing RNA-seq sequencing depth. Finally we take advantage of the "agnostic" approach of RNA-seq to discover areas of expression outside of annotated exons that show marked changes in expression following nerve injury.

Results

RNA-seq and microarrays largely agree in terms of the genes called as differentially expressed. However, RN

SUBMITTER: Perkins JR 

PROVIDER: S-EPMC4021616 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature