title: RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice.
abstract: BACKGROUND
  Dose-dependent differential gene expression provides critical information required for regulatory decision-making. The lower costs associated with RNA-Seq have made it the preferred technology for transcriptomic analysis. However, concordance between RNA-Seq and microarray analyses in dose response studies has not been adequately vetted.
  
  
  RESULTS
  We compared the hepatic transcriptome of C57BL/6 mice following gavage with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 μg/kg TCDD every 4 days for 28 days using Illumina HiSeq RNA-Sequencing (RNA-Seq) and Agilent 4 × 44 K microarrays using the same normalization and analysis approach. RNA-Seq and microarray analysis identified a total of 18,063 and 16,403 genes, respectively, that were expressed in the liver. RNA-Seq analysis for differentially expressed genes (DEGs) varied dramatically depending on the P1(t) cut-off while microarray results varied more based on the fold change criteria, although responses strongly correlated. Verification by WaferGen SmartChip QRTPCR revealed that RNA-Seq had a false discovery rate of 24% compared to 54% for microarray analysis. Dose-response modeling of RNA-Seq and microarray data demonstrated similar point of departure (POD) and ED50 estimates for common DEGs.
  
  
  CONCLUSIONS
  There was a strong correspondence between RNA-Seq and Agilent array transcriptome profiling when using the same samples and analysis strategy. However, RNA-Seq provided superior quantitative data, identifying more genes and DEGs, as well as qualitative information regarding identity and annotation for dose response modeling in support of regulatory decision-making.
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA. naultran@msu.edu.
authors.forename: Rance
authors.initials: R
authors.lastname: Nault
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA. kfader@msu.edu.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Fader
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA. tzachare@msu.edu.
authors.forename: Tim
authors.initials: T
authors.lastname: Zacharewski
mesh_terms: D000818:Animals; D004305:Dose-Response Relationship, Drug; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000187:drug effects; D008099:Liver / Q000187:drug effects*; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D000072317:Polychlorinated Dibenzodioxins / Q000008:administration & dosage* / Q000633:toxicity; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D000072317:Polychlorinated Dibenzodioxins