Battke, F., Herbig, A., Wentzel, A., Jakobsen, Ø. M., Bonin, M., Hodgson, D. A. (David A.), Wohlleben, W., Ellingsen, T. E. and Nieselt, K. (2011) A Technical Platform for Generating Reproducible Expression Data from Streptomyces coelicolor Batch Cultivations. In: Arabnia, H.R and Tran, Q-N., (eds.) Software Tools and Algorithms for Biological Systems. Advances in Experimental Medicine and Biology , Vol.696 . New York: Springer, pp. 3-15. ISBN 978-1-4419-7045-9

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Abstract

Streptomyces coelicolor, the model species of the genus Streptomyces, presents a complex life cycle of successive morphological and biochemical changes involving the formation of substrate and aerial mycelium, sporulation and the production of antibiotics. The switch from primary to secondary metabolism can be triggered by nutrient starvation and is of particular interest as some of the secondary metabolites produced by related Streptomycetes are commercially relevant. To understand these events on a molecular basis, a reliable technical platform encompassing reproducible fermentation as well as generation of coherent transcriptomic data is required. Here, we investigate the technical basis of a previous study as reported by Nieselt et at (BMC Genomics 11:10, 2010) in more detail, based on the same samples and focusing on the validation of the custom-designed rnicroarray as well as on the reproducibility of the data generated from biological replicates. We show that the protocols developed result in highly coherent transcriptomic measurements. Furthermore, we use the data to predict chromosomal gene clusters, extending previously known clusters as well as predicting interesting new clusters with consistent functional annotations.

Item Type:	Book Item
Subjects:	Q Science > Q Science (General)
Divisions:	Faculty of Science > Life Sciences (2010- )
Series Name:	Advances in Experimental Medicine and Biology
Journal or Publication Title:	Advances in Experimental Medicine and Biology
Publisher:	Springer
Place of Publication:	New York
ISBN:	978-1-4419-7045-9
ISSN:	0065-2598
Book Title:	Software Tools and Algorithms for Biological Systems
Editor:	Arabnia, H.R and Tran, Q-N.
Date:	2011
Volume:	Vol.696
Number of Pages:	13
Page Range:	pp. 3-15
Identification Number:	10.1007/978-1-4419-7046-6_1
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
URI:	http://wrap.warwick.ac.uk/id/eprint/42530

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