Unknown,Transcriptomics,Genomics,Proteomics

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Systematic Evaluation of Medium-Throughput mRNA Abundance Platforms

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 present ABI's OpenArray and qPCR systems. 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-41388 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Systematic evaluation of medium-throughput mRNA abundance platforms.

Prokopec Stephenie D SD Watson John D JD Waggott Daryl M DM Smith Ashley B AB Wu Alexander H AH Okey Allan B AB Pohjanvirta Raimo R Boutros Paul C PC

RNA (New York, N.Y.) 20121120 1

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 applications. 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 a high-throughput discovery platfo ...[more]

PMID: 23169800

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Dataset Information

Systematic Evaluation of Medium-Throughput mRNA Abundance Platforms

Publications

Systematic evaluation of medium-throughput mRNA abundance platforms.

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