Transcriptomics

Dataset Information

39

UV-C dose and time range finding study on Mouse Embryonic Fibroblasts (MEFs)


ABSTRACT: In molecular biology, the design of mechanistic experiments has to be optimized by considering statistical and biological principles. In contrast to statistical principles, biological principles of experimental design are not universally formulated. In an attempt to pinpoint generally acceptable rules, we investigated the importance of determining the optimal ranges of scale of i.e. dose and time in gene expression experiments. We propose a protocol for executing small scale, genome wide, range finding studies, covering a wide range of the potentially relevant part of the design space to find the optimal ranges of experimentation. This protocol is executed and a proof-of-concept is presented, where this approach is tested for both an in-vitro and an in-vivo study that aim to unravel DNA repair mechanisms provoked after UV radiation. We identified four challenges of range finding studies in omics experimentation; (1) the modularity of biological processes, (2) their dynamics, (3) the extent to which end-points indicate biological processes, and (4) the costs associated with the assays, which are all addressed by our approach. 48 MEF samples having various combinations of 9 timepoints and 6 UV-C Doses without replication were used

ORGANISM(S): Mus musculus  

SUBMITTER: Wendy Rodenburg  Conny van Oostrum   Annemieke de Vries   Timo M Breit   Wim A Ensink   Rob J Dekker   Martijs J Jonker   Oskar Bruning   Mark H de Jong   Han Rauwerda    

PROVIDER: E-GEOD-50930 | ArrayExpress | 2014-09-06

SECONDARY ACCESSION(S): GSE50930PRJNA219390

REPOSITORIES: GEO, ArrayExpress

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