|
| Status |
Public on May 31, 2016 |
| Title |
BHI+Fe_t5 over BHI_t5 (2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
BHI+Fe_t5: cells grown with supplemented iron in BHI+Fe until t5
|
| Organism |
Bacillus cereus ATCC 10987 |
| Characteristics |
strain: ATCC 10987
|
| Treatment protocol |
Cells were harvested at t5 and t12 hours of growth.
|
| Growth protocol |
Liquid cultures of B. cereus ATCC 10987 were grown in BHI, BHI+Fe, BHI+Bipy and BHI+Fe+Bipy in 12-well plates statically at 30°C. 3ml was grown in each well and 8 such wells were pulled together for RNA isolation.
|
| 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 |
BHI_t5: cells grown in BHI as control until t5
|
| Organism |
Bacillus cereus ATCC 10987 |
| Characteristics |
strain: ATCC 10987
|
| Treatment protocol |
Cells were harvested at t5 and t12 hours of growth.
|
| Growth protocol |
Liquid cultures of B. cereus ATCC 10987 were grown in BHI, BHI+Fe, BHI+Bipy and BHI+Fe+Bipy in 12-well plates statically at 30°C. 3ml was grown in each well and 8 such wells were pulled together for RNA isolation.
|
| 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 patterns were studied with and without iron starvation
|
| 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 was selected as the gene expression intensity.
|
| |
|
| Submission date |
Oct 15, 2015 |
| Last update date |
May 31, 2016 |
| Contact name |
Michiel Wels |
| E-mail(s) |
[email protected]
|
| Organization name |
NIZO food research
|
| Street address |
Kernhemseweg 2
|
| City |
Ede |
| ZIP/Postal code |
6718 ZB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL7681 |
| Series (1) |
| GSE74045 |
Transcriptome comparison between Bacillus cereus ATCC 10987 cells with and without iron starvation |
|
