|
| Status |
Public on Mar 31, 2013 |
| Title |
59A rep2 |
| Sample type |
RNA |
| |
|
| Source name |
59A
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: 59A
array: 1
block: 1
|
| Treatment protocol |
Fermentation condition was established with 230 g/L glucose + fructose, 5% lipid factor and 142 mg/L assimilable nitrogen in synthetic medium.
|
| Growth protocol |
59A control strain and 59A sch9-deleted strain used in this study were precultured in a nutrient medium containing Yeast Nitrogen Base (YNB) without amino acids (6.7 g/L) and glucose (20 g/L), for 24h at 28°C in Erlenmeyer flasks. The fermentation medium was inoculated at 1 106 cell/mL from preculture. Yeast cultures were carried out in fermenters (1.2 L, containing 1 L medium), with fermentation locks (CO2 bubbling outlets filled with water). Fermentation media were normally deaerated prior to inoculation by bubbling pure argon 5 min. Filling conditions were controlled and fermentations were carried out under anaerobic conditions with permanent stirring (300 rpm) under isothermal conditions (24°C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)
|
| |
|
| Hybridization protocol |
Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).
|
| Scan protocol |
The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7
|
| Description |
Gene expression in sample from 59A strain, biological rep 2
|
| Data processing |
Data normalization and statistical analysis were performed using R 2.14.2 software and the limma package. Normalization was done by the quantile method considering all arrays
|
| |
|
| Submission date |
Nov 05, 2012 |
| Last update date |
Mar 31, 2013 |
| Contact name |
Bruno Blondin |
| E-mail(s) |
bruno.blondin@supagro.inra.fr
|
| Organization name |
INRA
|
| Department |
UMR1083
|
| Lab |
SPO
|
| Street address |
2 place Pierre Viala
|
| City |
Montpellier |
| ZIP/Postal code |
34060 |
| Country |
France |
| |
|
| Platform ID |
GPL16244 |
| Series (1) |
| GSE42027 |
Impact of nutrient unbalances on wine alcoholic fermentation: nitrogen excess enhances yeast cell death in lipid-limited must |
|
