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Platform GPL5459 Query DataSets for GPL5459
Status Public on Oct 20, 2009
Title SBO_LAB_2k_version1
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 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.
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 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.
 
Contributor(s) Weckx S, Allemeersch J, Van der Meulen R, Vrancken G, De Vuyst L, Van Hummelen P
Submission date Jul 02, 2007
Last update date Oct 20, 2009
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 (94) GSM230193, GSM230194, GSM230195, GSM230196, GSM230197, GSM230198 
Series (7)
GSE9082 DNA validation of LAB 2k v2
GSE9140 RNA validation of LAB 2k v2
GSE15686 Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation

Data table header descriptions
ID
PROTEIN_ACCESSION GenBank accession number
GB_ACC nucleotide accession number
SPOT_ID
DESCRIPTION description
GENE_SYMBOL Gene symbol
TYPE type of probe (i.e., functional (FUNCT), identification (IDENT), or control (CONTROL))
SPECIES Organism
TAX_ID Taxonomy Id
EC_NUMBER EC-number
PATHWAY pathway
CROSSHYB_INFO Information on possible cross-hybridizations

Data table
ID PROTEIN_ACCESSION GB_ACC SPOT_ID DESCRIPTION GENE_SYMBOL TYPE SPECIES TAX_ID EC_NUMBER PATHWAY CROSSHYB_INFO
F000193 CAA10553 AJ131979.1 Beta-galactosidase FUNCT Lactobacillus plantarum 1590 3.2.1.23 chp
F000252 ZP_00323908 NZ_AAEV01000001.1 fructose-1,6-biphosphate aldolase FUNCT Pediococcus pentosaceus ATCC25745 278197 4.1.2.13 chp
F000295 ZP_00063410 NZ_AABH02000019.1 Phosphoglucose isomerase / glucose-6-phosphate isomerase FUNCT Leuconostoc mesenteroides subsp mesenteroides ATCC8293 203120 5.3.1.9 chp
F000438 NP_266925 NC_002662.1 mannose-6-phosphate isomerase ManA FUNCT Lactococcus lactis subsp lactis Il1403 272623 5.3.1.8 chp
F000601 AAC45780 U62095.1 alpha-amylase FUNCT Lactobacillus plantarum 1590 3.2.1.1 chp
F000611 AAB23068 S43266.1 alpha-amylase FUNCT Enterococcus faecalis 1351 3.2.1.1 chp
F000694 AAQ07045 AF496361.1 triose phosphate isomerase FUNCT Lactobacillus delbrueckii subsp lactis 29397 5.3.1.1 chp
F000863 NP_964768 NC_005362.1 Levansucrase FUNCT Lactobacillus johnsonii NCC533 257314 2.4.1.10 eps
F000866 AAS79426 AY504865.1 Dextransucrase FUNCT Leuconostoc mesenteroides 1245 2.4.1.5 eps
F000970 AAC45231 AF036485.2 EpsD EpsD FUNCT Lactococcus lactis subsp cremoris 1359 NULL eps
F001059 YP_194568 NC_006814.2 EpsJ EpsJ FUNCT Lactobacillus acidophilus NCFM 272621 NULL eps
F001093 AAP32714 AF142639.1 EpsX EpsX FUNCT Lactococcus lactis subsp cremoris 1359 NULL eps
F001223 NP_784310 NC_004567.1 Ornithine cabamoyltransferase argf FUNCT Lactobacillus plantarum WCFS1 220668 2.1.3.3 aamet
F001276 AAK05304 AE006353.1 histidinol-phosphate aminotransferase hisC FUNCT Lactococcus lactis subsp lactis Il1403 272623 2.6.1.9 aamet
F001284 CAA11270 AJ223331.1 Carbamate kinase ArcC FUNCT Enterococcus faecalis 1351 2.7.2.2 aamet
F001379 NP_784306 NC_004567.1 N-acetyl-gamma-glutamyl-phosphate reductase argC FUNCT Lactobacillus plantarum WCFS1 220668 1.2.1.38 aamet
F001387 NP_784308 NC_004567.1 acetyl glutamate kinase argB FUNCT Lactobacillus plantarum WCFS1 220668 2.7.2.8 aamet
F001411 NP_784309 NC_004567.1 Acetylornithine aminotransferase argD FUNCT Lactobacillus plantarum WCFS1 220668 2.6.1.11 aamet
F001439 NP_784307 NC_004567.1 Ornithine acetyltransferase / glutamate N-acetyltransferase argJ FUNCT Lactobacillus plantarum WCFS1 220668 2.3.1.35 aamet
F001641 AAD55378 AF149712.1 branched-chain alpha-keto acid dehydrogenase bkdABCD FUNCT Enterococcus faecalis 1351 aamet

Total number of rows: 2381

Table truncated, full table size 477 Kbytes.




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

Supplementary file Size Download File type/resource
GPL5459_complete_array_layout.txt.gz 135.7 Kb (ftp)(http) TXT

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