Transcriptomics

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UV-B dose and time range finding study on mouse biopsy skin samples


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. 57 skin biopt samples taken from 12 individual mice on 8 timepionts and for 6 different UV-B doses. Per mouse 5 skin biopts were samples in time

ORGANISM(S): Mus musculus  

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

PROVIDER: E-GEOD-51348 | ArrayExpress | 2014-09-01

SECONDARY ACCESSION(S): GSE51348PRJNA222796

REPOSITORIES: GEO, ArrayExpress

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