|
| Status |
Public on Aug 31, 2010 |
| Title |
control_2 |
| Sample type |
RNA |
| |
|
| Source name |
Xylella fastidiosa 9a5c biofilm, untreated control
|
| Organism |
Xylella fastidiosa 9a5c |
| Characteristics |
agent: untreated
dose: n/a
|
| Treatment protocol |
After 15 days of growth, 3 or 7 mM of CuSO4 or 10 or 80 µg/ml of tetracyclin were added to the experiments and after one day the total RNA were extracted. Controls were made withough any substance.
|
| Growth protocol |
Bacterial cells were grown in biofilm in PW medium for 15 days in flasks under shaking (130 rpm, 28oC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an nanodrop spectophotometer and Bioanalyser 2100.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following the standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following the standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following the standard operating protocol. See www.nimblegen.com.
|
| Description |
It is the second of three control biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 04, 2010 |
| Last update date |
Jul 21, 2010 |
| Contact name |
Alessandra Alves De Souza |
| E-mail(s) |
alessandra@centrodecitricultura.br
|
| Organization name |
Instituto Agronomico de Campinas
|
| Department |
Centro de Citricultura Sylvio Moreira
|
| Lab |
Citrus Biotechnology lab
|
| Street address |
Rod Anhanguera KM 158
|
| City |
Cordeiropolis |
| State/province |
Sao Paulo |
| ZIP/Postal code |
13490970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL10380 |
| Series (1) |
| GSE21645 |
New insights on resistance mechanisms to antimicrobial compounds in a plant pathogen biofilm |
|
