Project name: Lactiplantibacillus plantarum

Description: We ran for each studied culture (WCFS1 NZ7608 and NZ7603) one aerobe and one anaerobe batch cultivation and designed one experiment. The hybridization scheme of the experiment (6 arrays) was as follows: WCFS1_aerobe NZ7608-aerobe NZ7603-aerobe WCFS1_aerobe and then three extra hybridizations: WCFS1_anaerobe w WCFS1_aerobe; NZ7608_anaerobe NZ7608_aerobe; and NZ7603_anaerobe NZ7603_aerobe. In the experiment we compared (1) the effect of oxygen in each studied culture and (2) the difference in response toward aerobe and anaerobe conditions of each mutant compared to the wild typeKeywords: comparative genomic hybridizationOverall design: Per array two cDNA labeled targets were hybridized on custom designed L. plantarum WCFS1 11K Agilent oligo microarrays (GEO Acc. Nr. GPL4318) using the Agilent 60-mer oligo microarray processing protocol version 4.1. An oligo-microarray contained an average of 3 probes per transcript. Dried slides were scanned in the Scan Array Express (PerkinElmer Life Sciences; Packard Bioscience) for both Cy3 and Cy5 at 10 microns and a PMT Gain between 40-50%. Spot intensity data was normalized and quantified (average intensity) using a customized grid in ImaGene (BioDiscovery, Inc.). Signal intensities of all probes were corrected against background in BioArray Software Environment (BASE). The ratio of each probe (M) was defined as log [cy5 intensity/cy3 intensity] where cy3 is the wild type. Fold change (FC) is defined as 2M. For the statistical analysis we used Linear Models for Microarray Analysis (Limma) (R/limma). Significant transcripts were defined as transcripts with a False Discovery Rate (FDR) adjusted for the pvalues of less than 10% and FC = 1.5

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Industrial

Release date: 2007-08-16

Last updated: 2007-08-10