|
| Status |
Public on Jul 31, 2012 |
| Title |
ymoA mutant vs. YPIII wild type, replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ymoA knockout mutant
|
| Organism |
Yersinia pseudotuberculosis YPIII |
| Characteristics |
background strain: YPIII
genotype: ymoA null mutant
|
| 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 with Cy3 using the ULS fluorescent labelling kit (Kreatech, Germany).
|
| |
|
| Channel 2 |
| Source name |
wild type
|
| Organism |
Yersinia pseudotuberculosis YPIII |
| Characteristics |
background strain: YPIII
genotype: wild type
|
| 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 with Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).
|
| |
|
| |
| Hybridization protocol |
300ng of each Cy3- and Cy5-labelled RNA were mixed, fragmented and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions.
|
| Scan protocol |
Data were scanned at a resolution of 5μm using Axon GenePix Personal 4100A scanner 14, and features were extracted using the software package GenePix Pro 6.015.
|
| Data processing |
The processing was done using the software package "R" in combination with the “Bioconductor” software framework (www.bioconductor.de) (Gentleman et al., 2004). Preprocessing based on the marray package employing the read.GenePix function. Control code for probe selection was adapted to the custom-made Agilent microarray system and a quality control was performed to check for hybridization artifacts and large-scale differences between the microarrays of one experiment. A two-color intensity-dependent normalization (“Lowess” normalization) was applied.
|
| |
|
| Submission date |
Jan 12, 2012 |
| Last update date |
Jul 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) |
| GSE35043 |
Yersinia pseudotuberculosis ymoA mutant vs. wild type YPIII |
|
