|
| Status |
Public on Oct 05, 2016 |
| Title |
sef1 under 4 h iron starvation, replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Yeasts in SD medium, iron-free
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: sef1
time: 4 h
replicate: 3
|
| Treatment protocol |
For the time series, cultures were harvested by centrifugation and washed four times with iron-free SD, then incubated in iron-free SD.
|
| Growth protocol |
Strains were cultured overnight in SD, harvested by centrifugation and washed four times in iron-free water. Cells were adjusted to 1×10E7 cells/ml in iron-free SD (pH 5.8) supplemented with 5 µM FeCl3 and pre-grown for 4 h at 37°C and 180 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the RNAeasy Mini Kit (Qiagen) and quality was verified using the Agilent 2100 Bioanalyzer Nanochip system.
|
| Label |
Cy5
|
| Label protocol |
1 µg high-quality RNA was used to generate cRNA fluorescently labeled with Cy5 CTP (GE Healthcare) using the One-Color Quick Amp labeling kit (Agilent).
|
| |
|
| Channel 2 |
| Source name |
Yeast in YPD, log phase (common reference)
|
| Organism |
Nakaseomyces glabratus |
| Characteristics |
strain: ATCC2001
time: 4 h
|
| Treatment protocol |
For the time series, cultures were harvested by centrifugation and washed four times with iron-free SD, then incubated in iron-free SD.
|
| Growth protocol |
Strains were cultured overnight in SD, harvested by centrifugation and washed four times in iron-free water. Cells were adjusted to 1×10E7 cells/ml in iron-free SD (pH 5.8) supplemented with 5 µM FeCl3 and pre-grown for 4 h at 37°C and 180 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the RNAeasy Mini Kit (Qiagen) and quality was verified using the Agilent 2100 Bioanalyzer Nanochip system.
|
| Label |
Cy3
|
| Label protocol |
1 µg high-quality RNA was used to generate cRNA fluorescently labeled with Cy5 CTP (GE Healthcare) using the One-Color Quick Amp labeling kit (Agilent).
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized using the Gene Expression Hybridization Kit (Agilent) according to manufacturer's instructions.
|
| Scan protocol |
Scanned with a GenePix 4200AL (GenePix Pro 6.1, Auto PMT wavelengths 635/594, pixel size 5 µm)
|
| Data processing |
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
Oct 05, 2016 |
| Contact name |
Sascha Brunke |
| E-mail(s) |
sascha.brunke@hki-jena.de
|
| Organization name |
Hans-Knöll-Institut
|
| Department |
MPM
|
| Street address |
Beutenbergstr. 11a
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10713 |
| Series (1) |
| GSE84816 |
Candida glabrata WT and mutants under iron starvation |
|
