Title
Quenching of microbial samples for increased reliability of microarray data
Author
Pieterse, B.
Jellema, R.H.
van der Werf, M.J.
TNO Kwaliteit van Leven
Publication year
2006
Abstract
Messenger RNA levels change on a minutes scale due to both degradation and de novo transcription. Consequently, alterations in the transcript profiles that are not representative for the condition of interest are easily introduced during sample harvesting and work-up. In order to avoid these unwanted changes we have validated a - 45°C methanol-based quenching method for obtaining reliable and reproducible 'snapshot' samples of Lactobacillus plantarum cells for transcriptome analyses. Transcript profiles of cells harvested with the quenching method were compared with transcript profiles of cells that were harvested according to two different commonly applied protocols. Significant differences between the transcript profiles of cells harvested by the different methods from the same steady-state culture were observed. In total, 42 genes or operons were identified from which the transcript levels were altered when the cells were not immediately quenched upon harvesting. Among these, several have previously been associated with cold-shock response. Furthermore, the reproducibility of transcript profiles improved, as indicated by the fact that the variation in the data sets obtained from the quenched cells was smaller than in the data sets obtained from the cells that were harvested under non-quenched conditions. © 2005 Elsevier B.V. All rights reserved.
Subject
Biology
Biotechnology
Microarray data
Microbial samples
Quenching
messenger RNA
transcriptome
article
cytolysis
gene
hybridization
image analysis
Lactobacillus plantarum
microarray analysis
nonhuman
operon
priority journal
RNA isolation
steady state
technique
Lactobacillus
Methanol
Protein Array Analysis
Reproducibility of Results
RNA, Bacterial
RNA, Messenger
Transcription, Genetic
Lactobacillus plantarum
To reference this document use:
http://resolver.tudelft.nl/uuid:ecee9f23-4bfe-44b8-884d-759db782fb00
DOI
https://doi.org/10.1016/j.mimet.2005.04.035
TNO identifier
239127
ISSN
0167-7012
Source
Journal of Microbiological Methods, 64 (2), 207-216
Document type
article