|
| Status |
Public on Jul 28, 2015 |
| Title |
SH t1 WT biol1 over SH t1 rpoN_compl biol1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT cells grown with shaking until OD(600nm)=0.2
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
strain derivative: WT
|
| Treatment protocol |
Cells were harvested at above mentioned timepoints (see overall design) without any additional treatment.
|
| Growth protocol |
Liquid cultures of B. cereus ATCC14579 WT, ΔrpoN and ΔrpoN-comp strains were grown in BHI with aeration (200rpm) and statically in Erlenmeyer flasks at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were spinned down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen. RNA was extracted according to the RNAwiz (Ambion) protocol using Chloroform/isopropanol extraction. Residual DNA was enzymatically removed using the TURBO DNA-free (Ambion) kit following the instructions of the manufacturer.
|
| Label |
cy3
|
| Label protocol |
Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)
|
| |
|
| Channel 2 |
| Source name |
rpoN-comp complemented mutant cells grown with shaking until OD(600nm)=0.2
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
strain derivative: ΔrpoN-comp
|
| Treatment protocol |
Cells were harvested at above mentioned timepoints (see overall design) without any additional treatment.
|
| Growth protocol |
Liquid cultures of B. cereus ATCC14579 WT, ΔrpoN and ΔrpoN-comp strains were grown in BHI with aeration (200rpm) and statically in Erlenmeyer flasks at 30°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were spinned down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen. RNA was extracted according to the RNAwiz (Ambion) protocol using Chloroform/isopropanol extraction. Residual DNA was enzymatically removed using the TURBO DNA-free (Ambion) kit following the instructions of the manufacturer.
|
| Label |
cy5
|
| Label protocol |
Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed as described in Mols et al., 2013.
|
| Scan protocol |
Slides were scanned with Agilent G2505C scanner
|
| Description |
Expression profiles of the rpoN deletion mutant (ΔrpoN) and the complemented strain (ΔrpoN-comp) were compared to the parental strain (WT) at aerated growth t1
|
| Data processing |
Data were normalized using Lowess normalisation as available in MicroPrep and corrected for inter-slide differences. Median intensity of the different probes per gene and biological replicate was selected as the gene expression intensity.
|
| |
|
| Submission date |
Feb 12, 2015 |
| Last update date |
Jul 28, 2015 |
| Contact name |
Jos Boekhorst |
| E-mail(s) |
Jos.Boekhorst@nizo.com
|
| Organization name |
NIZO food research
|
| Street address |
Kernhemseweg 2
|
| City |
Ede |
| ZIP/Postal code |
6718 ZB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19768 |
| Series (1) |
| GSE65894 |
Transcriptome comparison between Bacillus cereus ATCC 14579 wildtype (WT), RpoN (Sigma 54) deletion mutant and the complemented strain. |
|
