|
| Status |
Public on Aug 01, 2011 |
| Title |
120 Min Treated Cy5 vs. Control Cy3 Rep. 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Streptococcus mutans, treated, 120 min
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
treatment: treated
cell type: biofilm
genotype: wildtype
time point: 120 min
|
| Treatment protocol |
biofilm cells were treated with 0.25 µg/ml carolacton, control wells without treatment
|
| Growth protocol |
biofilms were grown in THBS medium for 3.5 hours (initial OD600 = 0.05) in 24 well polystyrene plates (Greiner, Germany), than the medium was exchanged against fresh THBS supplemented with and without carolacton (0.25 µg/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany)
|
| Label |
Cy5
|
| Label protocol |
RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany)
|
| |
|
| Channel 2 |
| Source name |
Streptococcus mutans, untreated, 120 min
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
treatment: untreated
cell type: biofilm
genotype: wildtype
time point: 120 min
|
| Treatment protocol |
biofilm cells were treated with 0.25 µg/ml carolacton, control wells without treatment
|
| Growth protocol |
biofilms were grown in THBS medium for 3.5 hours (initial OD600 = 0.05) in 24 well polystyrene plates (Greiner, Germany), than the medium was exchanged against fresh THBS supplemented with and without carolacton (0.25 µg/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany)
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany)
|
| |
|
| |
| Hybridization protocol |
760 ng of each Cy3- and Cy5 labelled RNA was fracmented and hybridised to the microarray at 65°C for 16 h using the Agilent Hybridisation Chamber and Agilent Hybridisation Kit according to the manufacturer`s instructions.
|
| Scan protocol |
the array was scanned using the Agilent DNA Microarray Scanner at 5 µm resolution and the raw data were extracted using Agilent Feature Extraction software (V9.5)
|
| Description |
120 Min DyeSwap 1/2, Repl. 2
|
| Data processing |
The data were processed by Bioconductor packages written in R language (http://www.r-project.org). The linear models for microarray analysis (LIMMA) package was used for background correction, Loess normalisation of the two chanels of one array, quantile-normalisation between different arrays and identification of differentially expressed genes.
|
| |
|
| Submission date |
Jan 04, 2011 |
| Last update date |
Aug 01, 2011 |
| Contact name |
Michael Reck |
| E-mail(s) |
[email protected]
|
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Microbial Communication
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10540 |
| Series (1) |
| GSE26441 |
Kinetic analysis of carolacton regulated genes |
|
