|
| Status |
Public on Sep 21, 2010 |
| Title |
log phase_rep 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild type at logarithmic phase of growth
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
genotype/variation: wildtype
|
| Treatment protocol |
at normal growth conditons or under different stresses
|
| Growth protocol |
S. mutans strains were grown in THBY medium at 37°C aerobically (5% CO2 enriched)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).
|
| |
|
| Channel 2 |
| Source name |
rpoE knockout mutant at logarithmic phase of growth
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
genotype/variation: rpoE knockout
|
| Treatment protocol |
at normal growth conditons or under different stresses
|
| Growth protocol |
S. mutans strains were grown in THBY medium at 37°C aerobically (5% CO2 enriched)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy mini kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).
|
| |
|
| |
| Hybridization protocol |
900 ng of each Cy3- and Cy5-labeled RNA was fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.
|
| Scan protocol |
The arrays were scanned using the Agilent DNA Microarray Scanner, and the raw data were extracted using Agilent Feature Extraction software (v9.5).
|
| Description |
biological replicate 1 of 2, technical replicate 2 of 2, logarithmic phase of growth, mutant and wild type
|
| 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-normalization of the two channels of one array, quantile-normalization between different arrays and identification of differentially expressed genes.
|
| |
|
| Submission date |
Jun 14, 2010 |
| Last update date |
Sep 21, 2010 |
| Contact name |
Xiaoli Xue |
| E-mail(s) |
[email protected]
|
| Phone |
+49(0)53161813084
|
| Fax |
+49(0)53161813096
|
| Organization name |
Helmholtz Center for Infection Research
|
| Department |
Cell Biology
|
| Lab |
Microbial Communication
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| ZIP/Postal code |
D-38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10540 |
| Series (1) |
| GSE22333 |
The delta subunit of RNA polymerase, RpoE, is a global modulator of Streptococcus mutans environmental adaptation |
|
