|
| Status |
Public on Dec 28, 2018 |
| Title |
Caf905-2 (rep2) |
| Sample type |
RNA |
| |
|
| Source name |
Log-phase rep2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: Caf905-2 mutant
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Growth in Yeast Minimal Medium at 30 ºC and 150 rpm until early exponential phase (OD600 ~1.0).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen) was used, according to the manufacturer’s instructions. RNA quality based on Integrity Numbers (RIN) was checked with Agilent 2100 Bioanalyzer. RNA samples with RIN values > 8 were utilized in the microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by purification using Absolutely RNA Nanoprep Kit (Agilent). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes, according to the manufacturer's instructions. Subsequently, the samples were immediately hybridized onto Agilent Yeast Oligo Microarray (V2) 8x15K G4813 in a rotating Agilent hybridization oven at 65 °C for 17 h.
|
| Scan protocol |
Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Caf905-2 (2)
Gene expression at log-phase in Yeast Minimal Medium.
|
| Data processing |
The scanned images were analyzed using Feature Extraction Software 9.1 (Agilent) with default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Dec 27, 2018 |
| Last update date |
Dec 28, 2018 |
| Contact name |
Halil ibrahim KISAKESEN |
| E-mail(s) |
kisakesenhi@gmail.com
|
| Phone |
+905307831229
|
| Organization name |
Istanbul Technical University
|
| Department |
Molecular Biology, Genetics and Biotechnology
|
| Lab |
Yeast
|
| Street address |
ITU MOBGAM, SARIYER
|
| City |
Istanbul |
| State/province |
Istanbul |
| ZIP/Postal code |
34469 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL16244 |
| Series (1) |
| GSE124452 |
Transcriptomic analysis of a caffeine-resistant Saccharomyces cerevisiae strain obtained by evolutionary engineering |
|
