E-MEXP-3360 - Pathochip of Streptococcus spp surface proteins

Status
Released on 15 September 2011, last updated on 2 May 2014
Organism
Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae
Samples (21)
Arrays (2)
Protocols (8)
Description
In order to appreciate the presence of surface protein gene homologues in commensal species S. mitis and S. oralis, comparative genomic hybridization studies using DNA microarrays were performed with 8 S. mitis and 11 S. oralis from different geographic locations. The oligonucleotide microarray was designed based on the genomes of S. pneumoniae R6 and TIGR4 as well as S. mitis B6 to include genes of 63 cell surface proteins. The denatured genomic DNA of the S. mitis and S. oralis strains was labeled with Cy3-dCTP and control S. mitis B6 DNA was labeled with Cy5-dCTP. Hybridization was performed following the manufacturers recommendations using an hybridization temperature of 40C for 16 h. For data processing, microarrays were scanned on the laser scanner Pro Scan Array GX (PerkinElmer) with the low resolution of 50 µm using ScanArrayExpress Software version 4.0. Photomultiplier tube was adjusted to balance the two fluorescence channels and biochips were scanned with a resolution of 10 µm. After elimination of background values fluorescence intensity was determined. Signals that showed an intensity ratio of 0.3 and above were considered to be positive.
Experiment types
comparative genomic hybridization by array, comparative genome hybridization, in vitro, individual genetic characteristics, pathogenicity
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MEXP-3360.idf.txt
Sample and data relationshipE-MEXP-3360.sdrf.txt
Raw data (1)E-MEXP-3360.raw.1.zip
Array designsA-MEXP-1772.adf.txt, A-MEXP-2109.adf.txt
Links