E-GEOD-9082 - DNA validation of LAB 2k v2

Status
Submitted on 17 September 2007, released on 20 October 2009, last updated on 27 March 2012
Organism
Enterococcus faecalis, Enterococcus faecium, Lactobacillus acidophilus, Lactobacillus curvatus, Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus johnsonii, Lactobacillus paralimentarius, Lactobacillus plantarum, Lactobacillus pontis, Lactobacillus sakei, Lactobacillus sanfranciscensis, Lactococcus lactis, Leuconostoc mesenteroides
Samples (40)
Array (1)
Protocols (7)
Description
To study their metabolic potential in natural ecosystems, we developed a species-independent LAB microarray, containing 2,269 30-mer oligonucleotides, and targeting 406 genes that play a key role in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. Also, genes linked to negative traits such as antibiotic resistance and virulence are represented. This experiment is a validation experiment, where we hybridized labelled DNA from 20 LAB strains, covering 86% of all oligos. Keywords: Platform validation experiment All sampels were hybridized twice in the Cy3 channel. In the Cy5 channel no sample was hybridized.
Experiment type
comparative genomic hybridization by array 
Contact
Citation
Development and validation of a species-independent functional gene microarray that targets lactic acid bacteria. Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, Huys G, Vandamme P, Van Hummelen P, De Vuyst L.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-9082.idf.txt
Sample and data relationshipE-GEOD-9082.sdrf.txt
Raw data (1)E-GEOD-9082.raw.1.zip
Processed data (1)E-GEOD-9082.processed.1.zip
Array designA-GEOD-5459.adf.txt
Links