|
| Status |
Public on Jun 26, 2008 |
| Title |
subtilis_ccpNexp_wt3 |
| Sample type |
RNA |
| |
|
| Source name |
Bacillus subtilis cells, wild-type, glucose medium
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
wild-type strain 168 CA, whole cells grown in glucose medium, exponential phase (OD600 0.5)
|
| Biomaterial provider |
Laboratoire de Microbiologie et Genetique Moleculaire, Thiverval-Grignon, France
|
| Treatment protocol |
no particular treatment was performed on cells prior to extract preparation.
|
| Growth protocol |
Cells pellet for RNA extraction were obtained from cultures grown up to exponential growth phase (OD600=0.5) in TSS miminal medium (Fouet and Sonenshein, 1990) supplemented with 10g/L glucose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
High-quality RNA preparation, radiolabelled cDNA synthesis and hybridization were performed as previously described (Hauser et al., 1998; Eymann et al., 2002). Cells pellet for RNA extraction were obtained from cultures grown up to exponential growth phase (OD600=0.5).
|
| Label |
33P
|
| Label protocol |
cDNA labelling kit were provided by Sigma-Genosys and used as recommended. 2µg total RNA was used for labeled cDNA preparation in the presence of 2,5 µL [a-33P]-dCTP (10 µCi/µL).
|
| |
|
| Hybridization protocol |
Panorama B. subtilis gene macroarrays (Sigma-Genosys) containing full-length PCR products of all 4107 B. subtilis protein-coding genes in duplicate were prehybridized for 2h at 65C with 100 µg/mL herring sperm DNA, and then hybridized for 20h at 65C with the denatured radiolabelled cDNA
|
| Scan protocol |
The arrays were then exposed for 24 hours to an Imaging Plate and scanned with a STORM phosphoimager (GE Lifesciences), images of the hybridized arrays were processed and signal intensities quantified using the Array Vision software (Imaging Research, Canada)
|
| Description |
Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN (yqzB) non polar mutant.
Two-condition experiment, wt vs. ccpN mutant. 4 experiments with 3 independent RNA preparations and 3 sets of macroarrays.
|
| Data processing |
Data analysis was performed using Array Vision software (Imaging Research, Canada) for signals and background quantitations. The raw data were re-scaled to account for the differences in individual hybridization intensities.
|
| |
|
| Submission date |
Jun 24, 2008 |
| Last update date |
Jun 30, 2008 |
| Contact name |
Thierry Doan |
| E-mail(s) |
[email protected]
|
| Organization name |
INRA
|
| Department |
Microbiologie
|
| Lab |
Microbiologie et Genetique Moleculaire
|
| Street address |
INRA
|
| City |
Thiverval-Grignon |
| ZIP/Postal code |
78850 |
| Country |
France |
| |
|
| Platform ID |
GPL188 |
| Series (2) |
| GSE11873 |
Bacillus subtilis 168 cells: wild-type vs. ccpN (non polar) |
| GSE11937 |
Bacillus subtilis 168 cells: ccpN mutant and ccpN-yqfL double mutant analysis |
|
