title: SBO_LAB_2k_version1
status: Public on Oct 20 2009
contact.city: Leuven
contact.first: Rekin's
contact.last: Janky
contact.email: Nucleomics.Bioinformatics@vib.be
contact.address: Herestraat 49 Box 816
contact.department: Nucleomics Core
contact.country: Belgium
contact.institute: VIB
organism: 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
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 11,520 features (30-mer oligonucleotides) printed in a layout of 12 meta rows and 4 meta columns; consisting out of 16 rows and 15 columns per block.  The array measures the expression of 2,269 functional genes, spotted with four duplicates.
  A second group of oligos consists out of 96 identification oligos, also added with each four duplicates, resulting in 384 spots.
  The Lucidea Universal ScoreCard Controls (Amersham Biosciences Buckinghamshire, UK) are added. We added 10 probes, that assess the dynamic range and 8 ratio controls.  Each control was spotted in 16 block with 4 copies per block (i.e., 16x4=64 copies); making a total of 1,152 control spots on the chip.
  A set of 908 spots remained empty.
  The platform data table reflects a condensed representation of the array.  The complete array layout file representing the replicated features as well is linked as a supplementary file.
manufacture_protocol: All oligos were obtained from Isogen Life Science BV (Ijsselstein, The Netherlands) 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.