Transcriptome analysis reveals novel pain targets enriched in TRPV1(+) neurons.

<p>(A) qPCR quantification of TRPV1 mRNA levels in samples hybridized on microarrays (n = 4, p<0.001, One-way ANOVA). (B) Relative expression levels of TRPV1 mRNA determined by microarray hybridizations (n = 4, p<0.001, One-way ANOVA with Bonferroni's multiple comparisons test). (C) Correlation matrix of the expression level of all genes (normalized fluorescence intensities) detected using micorarrays. Clustering of overall gene expression is visible between RTX and capsaicin treated samples. (D) qPCR quantification of TRPV1 mRNA levels in samples used for RNA-Seq (n = 3, p<0.001, paired two-tailed t-test). (E) Relative expression levels of TRPV1 mRNA determined by RNA-Seq (n = 3, p<0.001, One-way ANOVA). (F) Overview of the number of target transcripts identified by microarray hybridizations and RNA-Seq. Raw fluorescence intensities of microarrays were background corrected, log2 transformed, normalized, and filtered for expressed genes (Illumina detection p-value <0.01 in at least one of the samples, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115731#s4" target="_blank">Material and Methods</a> sections for details). Sequencing was performed using a 5500xl SOLiD System resulting in 664 million reads in total (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115731#s4" target="_blank">Material and Methods</a> sections for details). The reads were filtered to remove ribosomal RNA, tRNAs, and vector sequences. The remaining reads mapped to 16590 genes of the reference genome (rn5). Read counts were transformed to RPKM values (Reads per kilo base per million), normalized, and filtered to remove weakly expressed transcripts (RPKM>0.1). P-values of differentially expressed genes identified with both methods were adjusted for multiple testing with Benjamini and Hochberg's method, adjusted p-values <0.05 were considered significant.