|
| Status |
Public on Nov 16, 2010 |
| Title |
EGD-e / ∆LiaSLM Replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
EGD-e ∆LiaSLM
|
| Organism |
Listeria monocytogenes EGD-e |
| Characteristics |
genotype: wild type
|
| Treatment protocol |
L. monocytogenes strains were grown under aerobic conditions in brain heart infusion (BHI from BD Biosciences, contains 2 g dextrose/l) at 37°C.
|
| Growth protocol |
bacteria were grown until OD600nm of 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the L. monocytogenes strains grown to an OD600 of 1.0 was extracted using the RNA-Mini-Kit (Seqlab, Göttingen, Germany) according to the manufacturer’s protocol. Residual DNA was removed on a column with RNase-free DNase (QIAGEN, Hilden, Germany) and TurboDNase (Ambion)
|
| Label |
cy5
|
| Label protocol |
30 µg of total RNA were primed with 9 µg Random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 20 mM each dATP, dTTP, dGTP, with 10 µM dCTP, 50 nmol Cy3/Cy5-labelled dCTP
|
| |
|
| Channel 2 |
| Source name |
EGD-e
|
| Organism |
Listeria monocytogenes EGD-e |
| Characteristics |
genotype: ∆LiaSLM
|
| Treatment protocol |
L. monocytogenes strains were grown under aerobic conditions in brain heart infusion (BHI from BD Biosciences, contains 2 g dextrose/l) at 37°C.
|
| Growth protocol |
bacteria were grown until OD600nm of 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the L. monocytogenes strains grown to an OD600 of 1.0 was extracted using the RNA-Mini-Kit (Seqlab, Göttingen, Germany) according to the manufacturer’s protocol. Residual DNA was removed on a column with RNase-free DNase (QIAGEN, Hilden, Germany) and TurboDNase (Ambion)
|
| Label |
cy3
|
| Label protocol |
30 µg of total RNA were primed with 9 µg Random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U SuperScript II RTase (Invitrogen), and 20 mM each dATP, dTTP, dGTP, with 10 µM dCTP, 50 nmol Cy3/Cy5-labelled dCTP
|
| |
|
| |
| Hybridization protocol |
The slides were hybridized according to the manufacturers protocol (BF-BIOlabs)
|
| Scan protocol |
slides were scanned using Axon GenePix 4200 Microarray scanner and analyzed using the Genepix Pro 6.0 software
|
| Description |
Biological replicate 2 of 5.
|
| Data processing |
normalized using vsn, limma in R
|
| |
|
| Submission date |
Sep 13, 2010 |
| Last update date |
Nov 16, 2010 |
| Contact name |
Frederike Fritsch |
| Organization name |
Uni Würzburg
|
| Street address |
Am Hubland
|
| City |
Würzburg |
| ZIP/Postal code |
97072 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10909 |
| Series (1) |
| GSE24107 |
The cell envelope stress response mediated by the LiaFSRLm three-component system of Listeria monocytogenes is controlled via the phosphatase activity of the bifunctional histidine kinase LiaSLm |
|
