title: A technical platform for generating reproducible expression data from Streptomyces coelicolor batch cultivations.
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 al. (BMC Genomics 11:10, 2010) in more detail, based on the same samples and focusing on the validation of the custom-designed microarray 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.
authors: Faculty of Science, Center for Bioinformatics Tubingen, University of Tubingen , Sand Tubingen, Germany. kay.nieselt@uni-tuebingen.de
authors: F
authors: F
authors: Battke
authors: A
authors: A
authors: Herbig
authors: A
authors: A
authors: Wentzel
authors: O M
authors: OM
authors: Jakobsen
authors: M
authors: M
authors: Bonin
authors: D A
authors: DA
authors: Hodgson
authors: W
authors: W
authors: Wohlleben
authors: T E
authors: TE
authors: Ellingsen
authors: K
authors: K
authors: Nieselt
mesh_terms: D001431:Bacteriological Techniques; D005285:Fermentation; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D005798:Genes, Bacterial; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D015203:Reproducibility of Results; D012984:Software; D048372:Streptomyces coelicolor / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*