|
| Status |
Public on Dec 14, 2012 |
| Title |
WT T1g vs ΔplcRa T1r |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT_1_T1
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
genotype/variation: wild type
developmental stage: B. cereus ATCC14579 wildtype cells were grown to 1 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)
|
| Growth protocol |
The type strain B. cereus ATCC14579, an ∆plcRa isogenic mutant strain and a strain enabling overexpressing of the plcRa gene (Wild-type strain harboring pHT315plcRa vector) were used throughout this study. Strains were grown in LB broth at 37°C, in flasks, with an aeration ratio of 10, on a rotary shaker at 175 rpm. Cultures were inoculated to an OD600 of 0.05 with cells in the vegetative phase in LB broth, and cell cultures were harvested 1h (t1) and 2h after (t2) the onset of stationary phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Trizol method as described by van Schaik et al., 2004
|
| Label |
Cy3
|
| Label protocol |
Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.
|
| |
|
| Channel 2 |
| Source name |
ΔplcRa_1_T1
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
genotype/variation: ΔplcRa
developmental stage: B. cereus ATCC14579 (plcRa deletion) cells were grown to 1 hour after entry into stationary growth phase (LB, 37 degrees Celcius, 175 rpm)
|
| Growth protocol |
The type strain B. cereus ATCC14579, an ∆plcRa isogenic mutant strain and a strain enabling overexpressing of the plcRa gene (Wild-type strain harboring pHT315plcRa vector) were used throughout this study. Strains were grown in LB broth at 37°C, in flasks, with an aeration ratio of 10, on a rotary shaker at 175 rpm. Cultures were inoculated to an OD600 of 0.05 with cells in the vegetative phase in LB broth, and cell cultures were harvested 1h (t1) and 2h after (t2) the onset of stationary phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Trizol method as described by van Schaik et al., 2004
|
| Label |
Cy5
|
| Label protocol |
Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.
|
| |
|
| |
| Hybridization protocol |
The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.
|
| Scan protocol |
Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, using the extended dynamic range scan mode and 10 micron scan resolution according to the Agilent protocol .
|
| Description |
US22502548_251734310035_S02_Bcereus14579_3rdDesign_2_1
WT vs ΔplcRa T1 biological duplo 1 of 2
|
| Data processing |
Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was analyzed with the Vampire webbased microarray suite.
|
| |
|
| Submission date |
Jul 08, 2011 |
| Last update date |
Dec 14, 2012 |
| Contact name |
Eugenie HUILLET |
| E-mail(s) |
eugenie.huillet@jouy.inra.fr
|
| Phone |
0033130833631
|
| Fax |
0033130438097
|
| Organization name |
INRA institute
|
| Department |
MICA
|
| Lab |
MICALIS-GME
|
| Street address |
La Minière INRA
|
| City |
Guyancourt |
| ZIP/Postal code |
78285 |
| Country |
France |
| |
|
| Platform ID |
GPL9493 |
| Series (1) |
| GSE30514 |
Characterization of PlcRa, a new PlcR-like regulator involved in oxidative stress response and cysteine metabolism during early stationary phase in Bacillus cereus |
|
