|
| Status |
Public on Mar 31, 2015 |
| Title |
WTD0_b |
| Sample type |
RNA |
| |
|
| Source name |
WTD_control medium (WTD0)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741
genotype/variation: WTD; expressing the AhPDF1.1b defensin
growth medium: control medium
array id: 1
array block id: 7
|
| Treatment protocol |
Plates were supplemented or not with ZnSO4 at the final concentration of 20 mM.
|
| Growth protocol |
WT yeast cells (BY4741; Mat a, his3∆1, leu2∆0, met15∆0, ura3∆0) expressing the empty pFL38H vector harboring a HIS3 marker gene and expressing or not the AhPDF1.1b plant defensin (accession number AY961376) under the yeast Triose Phosphate Isomerase promoter in plasmid pYX212 were plated at the 50 UFC/cm2 density on solid YNB-derived medium (1.43 g/l Yeast Nitrogen Base w/o amino acids w/o ammonium sulfate (Ref. 233520, Difco), 20 g/l glucose, 6.4 g/l NH4NO3, 50 mM succinic acid-KOH pH 4.5, 20 mg/l methionine, 60 mg/l leucine, 20 g/l agarose (Réf. D5, Euromedex)) and grown at 30°C until the colony diameters were 0.48 ± 0.02 mm
|
| 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 |
Yeast expressing the plant defensin and grown in control condition (WTD0) repetition 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 18, 2014 |
| Last update date |
Mar 31, 2015 |
| Contact name |
Pierre BERTHOMIEU |
| E-mail(s) |
berthomieu@supagro.inra.fr
|
| Organization name |
Montpellier SupAgro
|
| Department |
UMR BPMP
|
| Street address |
Place Viala
|
| City |
Montpellier |
| ZIP/Postal code |
34060 |
| Country |
France |
| |
|
| Platform ID |
GPL16244 |
| Series (1) |
| GSE63395 |
Separated and combined effects of the over-expression of a plant defensin and of a 20 mM Zn treatment on yeast. |
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