Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

NanoString analysis of a rat liver mRNA panel following TCDD treatment

ABSTRACT: Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms M-bM-^@M-^S NanoStringM-bM-^@M-^Ys nCounter Analysis System and ABIM-bM-^@M-^Ys OpenArray System M-bM-^@M-^S to gold-standard quantitative real-time RT-PCR. TCDD-sensitive (Long-Evans) and TCDD-resistant (Han/Wistar) rats were used in both time-course and dose response studies to asses the transcriptomic response to TCDD-insult. The time-course experiment saw animals recieve a single dose of 100ug/kg TCDD or corn oil vehicle followed by euthanasia and tissue collection at various time-points. Animals in the dose-response experiment recieved a single dose of TCDD at varying concentrations or corn oil vehicle, followed by euthanasia and tissue collection 19 hours post-treatment. Each treatment group contained 4-5 biologicial replicates.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Stephenie Prokopec

PROVIDER: E-GEOD-43251 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

TCDD dysregulation of 13 AHR-target genes in rat liver.

Watson John D JD Prokopec Stephenie D SD Smith Ashley B AB Okey Allan B AB Pohjanvirta Raimo R Boutros Paul C PC

Toxicology and applied pharmacology 20131216 3

Despite several decades of research, the complete mechanism by which 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other xenobiotic agonists of the aryl hydrocarbon receptor (AHR) cause toxicity remains unclear. While it has been shown that the AHR is required for all major manifestations of toxicity, the specific downstream changes involved in the development of toxic phenotypes remain unknown. Here we examine a panel of 13 genes that are AHR-regulated in many species and tissues. We profiled ...[more]

PMID: 24355419

Publication: 1/2

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Dataset Information

NanoString analysis of a rat liver mRNA panel following TCDD treatment

Publications

TCDD dysregulation of 13 AHR-target genes in rat liver.

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