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Status |
Public on Aug 31, 2010 |
Title |
control_2 |
Sample type |
RNA |
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Source name |
Xylella fastidiosa 9a5c biofilm, untreated control
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Organism |
Xylella fastidiosa 9a5c |
Characteristics |
agent: untreated dose: n/a
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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.
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Growth protocol |
Bacterial cells were grown in biofilm in PW medium for 15 days in flasks under shaking (130 rpm, 28oC)
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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.
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Label |
Cy3
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Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following the standard operating protocol. See www.nimblegen.com.
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Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following the standard operating protocol. See www.nimblegen.com.
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Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following the standard operating protocol. See www.nimblegen.com.
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Description |
It is the second of three control biological replicates used in this experiment, each from separate cultures.
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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.).
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Submission date |
May 04, 2010 |
Last update date |
Jul 21, 2010 |
Contact name |
Alessandra Alves De Souza |
E-mail(s) |
alessandra@centrodecitricultura.br
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Organization name |
Instituto Agronomico de Campinas
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Department |
Centro de Citricultura Sylvio Moreira
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Lab |
Citrus Biotechnology lab
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Street address |
Rod Anhanguera KM 158
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City |
Cordeiropolis |
State/province |
Sao Paulo |
ZIP/Postal code |
13490970 |
Country |
Brazil |
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Platform ID |
GPL10380 |
Series (1) |
GSE21645 |
New insights on resistance mechanisms to antimicrobial compounds in a plant pathogen biofilm |
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