|
| Status |
Public on Nov 29, 2011 |
| Title |
Propolis 5 min x ethanol 5 min Replicate 2 (dye swap) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
total RNA from BY4742 treated with propolis for 5 min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
|
| Treatment protocol |
The BY4742 cells were exposed to 0.125% (vol/vol) alcoholic propolis extract. The treatment was carried out for 5 and 10 min at 30°C with mechanical shaking (200 rpm). The samples were immediately frozen in liquid nitrogen and stored at ultra low temperature (-70oC) for further analysis of transcriptome.
|
| Growth protocol |
The yeast cells were growth in YPD liquid medium until the Exponential (9 h) growth phase. After this, the BY4742 cells were exposed to 0.125% (vol/vol) alcoholic propolis extract. The treatment was carried out for 5 and 10 min at 30°C with mechanical shaking (200 rpm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 or Cyanine-5 for 2 hours at 40 oC.
|
| |
|
| Channel 2 |
| Source name |
total RNA from BY4742 treated with ethanol for 5 min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
|
| Treatment protocol |
The BY4742 cells were exposed to 0.125% (vol/vol) alcoholic propolis extract. The treatment was carried out for 5 and 10 min at 30°C with mechanical shaking (200 rpm). The samples were immediately frozen in liquid nitrogen and stored at ultra low temperature (-70oC) for further analysis of transcriptome.
|
| Growth protocol |
The yeast cells were growth in YPD liquid medium until the Exponential (9 h) growth phase. After this, the BY4742 cells were exposed to 0.125% (vol/vol) alcoholic propolis extract. The treatment was carried out for 5 and 10 min at 30°C with mechanical shaking (200 rpm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 or Cyanine-5 for 2 hours at 40 oC.
|
| |
|
| |
| Hybridization protocol |
For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction
|
| Scan protocol |
Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).
|
| Description |
Dye Swap of biological replicate 2.
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test). Data in the matrices are log2 LOWESS normalized Cy5/Cy3 ratios.
|
| |
|
| Submission date |
Nov 28, 2011 |
| Last update date |
Nov 29, 2011 |
| Contact name |
Patricia Alves de Castro |
| Organization name |
USP
|
| Department |
Pharmaceuticals Sciences
|
| Lab |
Molecular Biology
|
| Street address |
Av. do Café
|
| City |
Ribeirão Preto |
| State/province |
São Paulo |
| ZIP/Postal code |
14.040.903 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL9825 |
| Series (1) |
| GSE33971 |
Saccharomyces cerevisiae and propolis sensitivity |
|
