NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL10874 Query DataSets for GPL10874
Status Public on Aug 01, 2011
Title SBO_LAB_2k_version2
Technology type spotted oligonucleotide
Distribution non-commercial
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
Manufacturer VIB Microarray Facility
Manufacture protocol The oligos were obtained from Isogen Life Science BV and Sigma Genosys and diluted to 25 µM in 100 mM Na-Phosphate buffer plus 0.000675% sarcosyl (Sigma-Aldrich). A MicroGrid II spotter (Genomic Solutions, Huntingdon, United Kingdom) was used to spot the oligos using 10K pins on CodeLink™ Activated Slides (GE Healthcare, Bucks, United Kingdom). After spotting, the CodeLink™ Activated Slides were placed in a humid chamber containing saturated NaCl for minimal 24 h. Unused active groups were blocked with preheated blocking solution (50 mM ethanolamine, 0.1M Tris pH=9.0) at 50 °C for 30 min. Slides were rinsed twice with MilliQ water and washed with preheated 4xSSC, 0.1% SDS at 50 °C for 30 min in a shaking water bath. Slides were rinsed with MilliQ water and dried by centrifugation at 800 rpm for 3 min.
Support glass
Coating aminosilane
 
Description This species-independent microarray for Lactic Acid Bacteria (LAB) enables to assess the expression of genes that play a key role in the production of sugar carbolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. The array design contains 20,160 features (30-mer oligonucleotides) printed in a layout of 12 meta rows and 4 meta columns; consisting out of 20 rows and 21 columns per block. The array measures the expression of 6,209 functional genes. All oligonucleotides were spotted with three duplicates, except for 16 oligonucleotides which had 6 replicates. The Lucidea Universal ScoreCard Controls (Amersham Biosciences Buckinghamshire, UK) are added (864 spots). A set of 621 spots remained empty.
 
Web link http://www.microarrays.be
Contributor(s) Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, De Vuyst L, Van Hummelen P
Submission date Sep 02, 2010
Last update date Aug 01, 2011
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
 
Samples (10) GSM590050, GSM590051, GSM590052, GSM590053, GSM590054, GSM590055 
Series (1)
GSE23945 Lactobacillus plantarum IMDO 130201, a wheat sourdough isolate, adapts to growth in wheat sourdough simulation medium at different pH values through differential gene expression

Data table header descriptions
ID
GB_RANGE nucleotide accession number
PT_ACC GenBank accession number
DESCRIPTION description
ORF Gene symbol
ORGANISM Organism
TAXID Taxonomy Id
EC_NUMBER EC-number
PATHWAY pathway
CROSSHYB_INFO Information on possible cross-hybridizations

Data table
ID GB_RANGE PT_ACC DESCRIPTION ORF ORGANISM TAXID EC_NUMBER PATHWAY CROSSHYB_INFO
F000001 AF400064.1 AAK85432 Alcohol dehydrogenase Lactobacillus sakei 1599 1.1.1.1 chp Lactobacillus sakei sakei 23K
F000010 CP000024.1 AAV60549 Alcohol dehydrogenase Streptococcus thermophilus CNRZ1066 299768 1.1.1.1 chp Streptococcus thermophilus LMG18311
F000012 CP000024.1 AAV60548 Alcohol dehydrogenase Streptococcus thermophilus CNRZ1066 299768 1.1.1.1 chp Streptococcus thermophilus LMG18311
F000014 CP000023.1 AAV60601 Alcohol dehydrogenase Streptococcus thermophilus LMG18311 264199 1.1.1.1 chp Streptococcus thermophilus LMD-9
F000015 CP000023.1 AAV60550 Alcohol dehydrogenase Streptococcus thermophilus LMG18311 264199 1.1.1.1 chp Streptococcus thermophilus CNRZ1066
F000021 AF328838.1 CAD62945 L-Lactate dehydrogenase Lactobacillus plantarum 1590 1.1.1.27 chp Lactobacillus plantarum WCFS1
F000023 AJ293008.1 CAC51461 L-Lactate dehydrogenase Lactobacillus plantarum 1590 1.1.1.27 chp Lactobacillus plantarum WCFS1
F000025 X70927.1 CAA50278 L-Lactate dehydrogenase Pediococcus acidilactici 1254 1.1.1.27 chp Enterococcus faecium DO
F000027 CP000023.1 AAV60912 L-Lactate dehydrogenase Streptococcus thermophilus LMG18311 264199 1.1.1.27 chp Streptococcus thermophilus LMD-9
F000029 AY820162.1 AAV68348 L-Lactate dehydrogenase Leuconostoc mesenteroides 1245 1.1.1.27 chp Leuconostoc mesenteroides mesenteroides
F000031 U26688.1 AAD03812 L-Lactate dehydrogenase Lactobacillus sakei 1599 1.1.1.27 chp Lactobacillus sakei sakei 23K
F000032 NC_005362.1 AAS08257 L-Lactate dehydrogenase Lactobacillus johnsonii NCC533 257314 1.1.1.27 chp Lactococcus lactis cremoris MG1363
F000033 Z81318.1 CAB03618 L-Lactate dehydrogenase Lactobacillus helveticus 1587 1.1.1.27 chp Lactobacillus helveticus DPC4571
F000034 D13405.1 AAV62824 L-Lactate dehydrogenase Streptococcus thermophilus 1308 1.1.1.27 chp Streptococcus thermophilus LMD-9
F000035 DQ225115.1 ABJ71272 L-Lactate dehydrogenase Lactobacillus rhamnosus 47715 1.1.1.27 chp Lactobacillus rhamnosus HN001
F000045 AJ582212.1 CAE46650 6-phosphogluconate dehydrogenase Lactobacillus curvatus 28038 1.1.1.44 chp Lactobacillus reutri DSM 20016
F000048 NZ_AAGO01000002.1 6-phosphogluconate dehydrogenase Lactococcus lactis cremoris SK11 272622 1.1.1.44 chp Lactococcus lactis cremoris MG1363
F000063 CP000024.1 AAV62627 acetoin dehydrogenase - E1 complex - alpha subunit Streptococcus thermophilus CNRZ1066 299768 1.1.1.5 chp Streptococcus thermophilus LMD-9
F000065 CP000024.1 AAV60576 acetoin dehydrogenase - E1 complex - alpha subunit Streptococcus thermophilus CNRZ1066 299768 1.1.1.5 chp Streptococcus thermophilus LMG18311
F000070 CP000023.1 AAV60701 acetoin dehydrogenase - E1 complex - alpha subunit Streptococcus thermophilus LMG18311 264199 1.1.1.5 chp Streptococcus thermophilus CNRZ1066

Total number of rows: 6209

Table truncated, full table size 796 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap