|
| Status |
Public on Dec 31, 2012 |
| Title |
crpvsYPIII_GEO_sample01 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
YPIII pIB1 wild type
|
| Organism |
Yersinia pseudotuberculosis YPIII |
| Characteristics |
strain: YPIII pIB1 wild type
|
| Growth protocol |
Y. pseudotuberculosis strains were grown in LB medium at 25°C to stationary phase (OD600 = 3.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the SV Total RNA Isolation System (Promega)
|
| Label |
Cy5
|
| Label protocol |
RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)
|
| |
|
| Channel 2 |
| Source name |
YPIII pIB1 crp mutant
|
| Organism |
Yersinia pseudotuberculosis YPIII |
| Characteristics |
strain: YPIII pIB1 crp mutant
|
| Growth protocol |
Y. pseudotuberculosis strains were grown in LB medium at 25°C to stationary phase (OD600 = 3.5)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the SV Total RNA Isolation System (Promega)
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)
|
| |
|
| |
| Hybridization protocol |
300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions
|
| Scan protocol |
The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6
|
| Description |
Biological replicate 1 of 4.
|
| Data processing |
The data were processed by R16 in combination with Bioconductor. Thereby, preprocessing was based on the marray package employing initially the read.GenePix function. Control code for probe selection was adapted due to Agilent purposes and quality control was performed to check for hybridization artifacts as well as to avoid large scale differences between the microarrays of one experiment. Lowess normalization was applied for two-color intensity-dependent normalization within each microarray and if necessary supplemented by scale normalization between different microarrays. Further diagnostic plots showing normalization results were created for quality assessment. Afterwards, differentially expressed genes were obtained using the limma package and the lmFit function for linear modeling, eBayes for significance calculations and topTable for the extraction of the differential expressed genes. Since every gene on the microarray was represented at least by three probes, overall fold-changes were summarized on the calculation of the median value for all mating probes
|
| |
|
| Submission date |
Nov 09, 2012 |
| Last update date |
Dec 31, 2012 |
| Contact name |
Ann Kathrin Heroven |
| E-mail(s) |
Annkathrin.Heroven@helmholtz-hzi.de
|
| Phone |
+49-(0)53161815705
|
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Molecular Infection Biology
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| State/province |
Niedersachsen |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15095 |
| Series (1) |
| GSE42206 |
Crp induces switching of the CsrB and CsrC RNAs in Yersinia pseudotuberculosis and links nutritional status to virulence |
|
