|
| Status |
Public on Dec 21, 2015 |
| Title |
Bacteria_acid_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
bacterial cells, acidic shock
|
| Organism |
Mesorhizobium japonicum MAFF 303099 |
| Characteristics |
treatment: acidic shock
|
| Treatment protocol |
Cells grown overnight at 28 ºC and maintained at 28 ºC for the 30 min were used as control. For acidic shock experiments, cells grown overnight at 28 ºC were subjected to an acidic shock of pH 3 at 28 ºC for 30 min.
|
| Growth protocol |
10 ml of cells with an OD(540 nm)=0.3, which corresponds to approximately 6x10exp8 cells per ml were used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen) manufacturer's protocol
mRNA enrichment protocol: MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) - Manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
aRNA amplification protocol: MessageAmp™ II-Bacteria Kit (Ambion) - Manufacturer's protocol
Quick Amp Labeling Kit (Agilent) - Manufacturer's protocol
|
| |
|
| Hybridization protocol |
One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol
|
| Scan protocol |
One-Color Microarray-Based Gene Expression Analysis (Agilent) - Manufacturer's protocol
|
| Data processing |
The signal intensity for each spot was extracted using QuantArray Analysis Software (GSI Lumonics). Analysis of raw data was performed using BRB-ArrayTools v3.4.0, where each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. The normalized dataset was then subjected to statistical analysis and clustering using MeV software to identified the diferencially expressed genes. The same dataset was also used to calculate the M-value and Fold-change variation.
|
| |
|
| Submission date |
Jan 16, 2013 |
| Last update date |
Dec 21, 2015 |
| Contact name |
Marta Laranjo |
| E-mail(s) |
[email protected]
|
| Organization name |
Universidade de Evora
|
| Department |
ICAAM
|
| Street address |
Apartado 94
|
| City |
Evora |
| ZIP/Postal code |
7002-554 Evora |
| Country |
Portugal |
| |
|
| Platform ID |
GPL16511 |
| Series (1) |
| GSE43527 |
Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an acidic shock |
|
