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Series GSE9082 Query DataSets for GSE9082
Status Public on Oct 20, 2009
Title DNA validation of LAB 2k v2
Platform organisms Leuconostoc mesenteroides; Oenococcus oeni; Pediococcus acidilactici; Pediococcus pentosaceus; Staphylococcus aureus; Streptococcus thermophilus; Enterococcus faecalis; Enterococcus faecium; Enterococcus hirae; Lactococcus lactis; Lactobacillus acidophilus; Levilactobacillus brevis; Lentilactobacillus buchneri; Lacticaseibacillus casei; Weissella confusa; Lactobacillus delbrueckii; Lactobacillus helveticus; Lentilactobacillus hilgardii; Lactiplantibacillus pentosus; Lactiplantibacillus plantarum; Lactobacillus gasseri; Lacticaseibacillus paracasei; Limosilactobacillus reuteri; Latilactobacillus sakei; Companilactobacillus alimentarius; Lactobacillus amylovorus; Companilactobacillus farciminis; Limosilactobacillus fermentum; Fructilactobacillus fructivorans; Fructilactobacillus sanfranciscensis; Bifidobacterium; Brevibacterium linens; Latilactobacillus curvatus; Lactobacillus johnsonii; Leuconostoc citreum; Leuconostoc pseudomesenteroides; Limosilactobacillus pontis; Enterococcus casseliflavus; Mammaliicoccus lentus; Limosilactobacillus panis; Lacticaseibacillus rhamnosus; Lactobacillus crispatus; Enterococcus mundtii; Lactiplantibacillus paraplantarum; Companilactobacillus paralimentarius; Limosilactobacillus frumenti; Lentilactobacillus parabuchneri; Companilactobacillus mindensis; Furfurilactobacillus rossiae
Sample organisms Leuconostoc mesenteroides; Enterococcus faecalis; Enterococcus faecium; Lactococcus lactis; Lactobacillus acidophilus; Lactobacillus delbrueckii; Lactiplantibacillus plantarum; Latilactobacillus sakei; Limosilactobacillus fermentum; Fructilactobacillus sanfranciscensis; Latilactobacillus curvatus; Lactobacillus johnsonii; Limosilactobacillus pontis; Companilactobacillus paralimentarius
Experiment type Genome variation profiling by array
Summary 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
 
Overall design All sampels were hybridized twice in the Cy3 channel. In the Cy5 channel no sample was hybridized.
 
Citation(s) 19684161
Submission date Sep 18, 2007
Last update date Mar 17, 2012
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platforms (1)
GPL5459 SBO_LAB_2k_version1
Samples (40)
GSM230193 4140
GSM230194 4141
GSM230195 4142
Relations
BioProject PRJNA102605

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9082_RAW.tar 6.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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