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Series GSE15391 Query DataSets for GSE15391
Status Public on Mar 16, 2010
Title Universal microarray for pattern-based bacterial species identification
Platform organism synthetic construct
Sample organisms Pantoea agglomerans; Micrococcus luteus; Escherichia coli B; Pantoea stewartii; Escherichia coli K-12; Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Experiment type Genome variation profiling by array
Summary Microarrays have become a powerful tool for DNA-based molecular diagnostics and identification of pathogens. However, most of them target a limited range of organisms and are generally based on only one or very few genes for organism identification. Although such microarrays are proven tools for species identification, they suffer from the fact that identification is only possible for organisms for which probes were specifically pre-developed. Furthermore, this approach often leads to problems with taxonomic-level resolution with insufficient diagnostic differences between closely related taxa found in the commonly used DNA sequences. An alternative strategy is to use the hybridisation pattern generated by many different anonymous markers distributed over the entire genome for identification based on comparison to a type database. We realised this strategy using a high density microarray containing 95,000 different 13-mer probes. Here, we demonstrate the specificity of our microarray based on results obtained with nine different bacterial species and strains. The hybridisation patterns allowed clear differentiation at the strain and even variant level. The reproducibility of our system was high as shown by high correlation coefficients between replicates, despite the occurrence of mismatch hybridisation. The results indicate the potential for identification of all bacterial taxa at the subspecies level using our universal microarray.
 
Overall design Hybridisation patterns of DNA from bacterial type strains (E. coli strains K12 and B, Pantoea agglomerans strains ATCC27155T and C9-1, Pantoea stewartii pv stewartii strain DC283, Salmonella Typhimurium strains LT2 and DT204 and Micrococcus luteus) were compared to each other. Using GeneSpring v7.3.1, cluster analyses were performed as well as ANOVA in order to determine the more discriminative probes out of our 95,000-probe panel.
 
Contributor(s) Pasquer F, Pelludat C, Duffy B, Frey JE
Citation(s) 20163710
Submission date Mar 25, 2009
Last update date Mar 21, 2012
Contact name Frederique Pasquer
E-mail(s) frederique.pasquer@acw.admin.ch
Phone +41 44 783 64 24
Organization name Agroscope Changins-Waedenswil Research Station ACW
Department Plant Protection
Lab 4
Street address Schloss
City Waedenswil
ZIP/Postal code 8820
Country Switzerland
 
Platforms (1)
GPL8295 ACW-universal-95000-v2
Samples (23)
GSM416612 E. coli strain B-a
GSM416613 E. coli strain B-b
GSM416614 E. coli strain K12-a
Relations
BioProject PRJNA117129

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
GSE15391_RAW.tar 143.3 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table

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