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A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure

In transcriptomics research, design for experimentation by carefully considering biological, technological, practical and statistical aspects is very important, because the experimental design space is essentially limitless. Usually, the ranges of variable biological parameters of the design space a...

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Autores principales: Bruning, Oskar, Rodenburg, Wendy, van Oostrom, Conny T., Jonker, Martijs J., de Jong, Mark, Dekker, Rob J., Rauwerda, Han, Ensink, Wim A., de Vries, Annemieke, Breit, Timo M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019648/
https://www.ncbi.nlm.nih.gov/pubmed/24823911
http://dx.doi.org/10.1371/journal.pone.0097089
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author Bruning, Oskar
Rodenburg, Wendy
van Oostrom, Conny T.
Jonker, Martijs J.
de Jong, Mark
Dekker, Rob J.
Rauwerda, Han
Ensink, Wim A.
de Vries, Annemieke
Breit, Timo M.
author_facet Bruning, Oskar
Rodenburg, Wendy
van Oostrom, Conny T.
Jonker, Martijs J.
de Jong, Mark
Dekker, Rob J.
Rauwerda, Han
Ensink, Wim A.
de Vries, Annemieke
Breit, Timo M.
author_sort Bruning, Oskar
collection PubMed
description In transcriptomics research, design for experimentation by carefully considering biological, technological, practical and statistical aspects is very important, because the experimental design space is essentially limitless. Usually, the ranges of variable biological parameters of the design space are based on common practices and in turn on phenotypic endpoints. However, specific sub-cellular processes might only be partially reflected by phenotypic endpoints or outside the associated parameter range. Here, we provide a generic protocol for range finding in design for transcriptomics experimentation based on small-scale gene-expression experiments to help in the search for the right location in the design space by analyzing the activity of already known genes of relevant molecular mechanisms. Two examples illustrate the applicability: in-vitro UV-C exposure of mouse embryonic fibroblasts and in-vivo UV-B exposure of mouse skin. Our pragmatic approach is based on: framing a specific biological question and associated gene-set, performing a wide-ranged experiment without replication, eliminating potentially non-relevant genes, and determining the experimental ‘sweet spot’ by gene-set enrichment plus dose-response correlation analysis. Examination of many cellular processes that are related to UV response, such as DNA repair and cell-cycle arrest, revealed that basically each cellular (sub-) process is active at its own specific spot(s) in the experimental design space. Hence, the use of range finding, based on an affordable protocol like this, enables researchers to conveniently identify the ‘sweet spot’ for their cellular process of interest in an experimental design space and might have far-reaching implications for experimental standardization.
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spelling pubmed-40196482014-05-16 A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure Bruning, Oskar Rodenburg, Wendy van Oostrom, Conny T. Jonker, Martijs J. de Jong, Mark Dekker, Rob J. Rauwerda, Han Ensink, Wim A. de Vries, Annemieke Breit, Timo M. PLoS One Research Article In transcriptomics research, design for experimentation by carefully considering biological, technological, practical and statistical aspects is very important, because the experimental design space is essentially limitless. Usually, the ranges of variable biological parameters of the design space are based on common practices and in turn on phenotypic endpoints. However, specific sub-cellular processes might only be partially reflected by phenotypic endpoints or outside the associated parameter range. Here, we provide a generic protocol for range finding in design for transcriptomics experimentation based on small-scale gene-expression experiments to help in the search for the right location in the design space by analyzing the activity of already known genes of relevant molecular mechanisms. Two examples illustrate the applicability: in-vitro UV-C exposure of mouse embryonic fibroblasts and in-vivo UV-B exposure of mouse skin. Our pragmatic approach is based on: framing a specific biological question and associated gene-set, performing a wide-ranged experiment without replication, eliminating potentially non-relevant genes, and determining the experimental ‘sweet spot’ by gene-set enrichment plus dose-response correlation analysis. Examination of many cellular processes that are related to UV response, such as DNA repair and cell-cycle arrest, revealed that basically each cellular (sub-) process is active at its own specific spot(s) in the experimental design space. Hence, the use of range finding, based on an affordable protocol like this, enables researchers to conveniently identify the ‘sweet spot’ for their cellular process of interest in an experimental design space and might have far-reaching implications for experimental standardization. Public Library of Science 2014-05-13 /pmc/articles/PMC4019648/ /pubmed/24823911 http://dx.doi.org/10.1371/journal.pone.0097089 Text en © 2014 Bruning et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Bruning, Oskar
Rodenburg, Wendy
van Oostrom, Conny T.
Jonker, Martijs J.
de Jong, Mark
Dekker, Rob J.
Rauwerda, Han
Ensink, Wim A.
de Vries, Annemieke
Breit, Timo M.
A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
title A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
title_full A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
title_fullStr A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
title_full_unstemmed A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
title_short A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
title_sort range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine uv exposure
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019648/
https://www.ncbi.nlm.nih.gov/pubmed/24823911
http://dx.doi.org/10.1371/journal.pone.0097089
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