|
| Status |
Public on Dec 30, 2016 |
| Title |
Ketoconazole 2 uM 5-R2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
antifungal treatment-high concentration
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: 2.5 uM ketoconazole
genetic background: BY4742
|
| Treatment protocol |
Yeast cells were treated in YPD (pH 4.8) supplemented with the antifungal at the indicated concentration or with DMSO andincubated at 28 °C with shaking for 4 h.
|
| Growth protocol |
Yeast cells were stored in glycerol 15% at -80°C, then tawned and growth in YPD (pH 4.8). The treatments were carried out after at least two inoculations to let cells recover.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from about 1 *109 cells using the hot acid phenol/chloroform protocol. RNAs were quantified spectrophotometrically using Nanodrop and by measuring the absorbance at 230, 260, and 280 nm and then calculating the 260/230 and 260/280 ratios and considering good data to be values of 1.8–2.2. RNA integrity was checked by electrophoresis in 1% agarose gel stained with ethidium bromide.
|
| Label |
Cy5
|
| Label protocol |
The labeling method used was the indirect method described by DeRisi (see the University of California San Francisco DeRisi laboratory Web site).
|
| |
|
| Channel 2 |
| Source name |
control treatment
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: DMSO
genetic background: BY4742
|
| Treatment protocol |
Yeast cells were treated in YPD (pH 4.8) supplemented with the antifungal at the indicated concentration or with DMSO andincubated at 28 °C with shaking for 4 h.
|
| Growth protocol |
Yeast cells were stored in glycerol 15% at -80°C, then tawned and growth in YPD (pH 4.8). The treatments were carried out after at least two inoculations to let cells recover.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from about 1 *109 cells using the hot acid phenol/chloroform protocol. RNAs were quantified spectrophotometrically using Nanodrop and by measuring the absorbance at 230, 260, and 280 nm and then calculating the 260/230 and 260/280 ratios and considering good data to be values of 1.8–2.2. RNA integrity was checked by electrophoresis in 1% agarose gel stained with ethidium bromide.
|
| Label |
Cy3
|
| Label protocol |
The labeling method used was the indirect method described by DeRisi (see the University of California San Francisco DeRisi laboratory Web site).
|
| |
|
| |
| Hybridization protocol |
Arrays were hybridized as described by the manufacturer. Hybridization took place at 63 °C for 14–16 h.
|
| Scan protocol |
Fluorescent cDNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments), using the GenePixPro6.1 software package to quantify microarray fluorescence.
|
| Data processing |
Data were normalized using the limma R package and DEGs (Differentially Expressed Genes) were identified with the RankProduct R package
|
| |
|
| Submission date |
Nov 20, 2012 |
| Last update date |
Dec 30, 2016 |
| Contact name |
Irene Stefanini |
| E-mail(s) |
stefanini.irene@gmail.com
|
| Organization name |
University of Turin
|
| Street address |
via Accademia Albertina
|
| City |
Torino |
| ZIP/Postal code |
10123 |
| Country |
Italy |
| |
|
| Platform ID |
GPL7542 |
| Series (1) |
| GSE42418 |
Expression analysis of novel and known antifungal drugs using S. cerevisiae as a model |
|
