|
| Status |
Public on Sep 05, 2015 |
| Title |
Hybrid between S. cerevisiae and S. kudriavzevii VIN7 replicate A, fermentation at 28ºC |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
yeast cells from wine fermentation at 28C
|
| Organism |
Saccharomyces cerevisiae x Saccharomyces kudriavzevii |
| Characteristics |
strain: VIN7
growth phase: Beginning of stationary phase
|
| Growth protocol |
Wine fermentations in Tempranillo must at 12C or 28C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).
|
| Label |
Cy3
|
| Label protocol |
2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA). The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.
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| |
|
| Channel 2 |
| Source name |
yeast cells from wine fermentation at 28C
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Lalvin T73
growth phase: Beginning of stationary phase
|
| Growth protocol |
Wine fermentations in Tempranillo must at 12C or 28C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).
|
| Label |
Cy5
|
| Label protocol |
2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA). The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight. (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).
|
| Scan protocol |
Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.
|
| Description |
Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate A
|
| Data processing |
Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found. Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated.
Genes with a two-fold log2 ratio values were considered to be significantly expressed.
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| |
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| Submission date |
Jul 19, 2011 |
| Last update date |
Sep 05, 2015 |
| Contact name |
Amparo Gamero |
| E-mail(s) |
amparo.gamerolluna@gmail.com
|
| Organization name |
IATA-CSIC
|
| Department |
Food Biotechnology
|
| Street address |
Avda. Agustín Escardino 7
|
| City |
Paterna |
| State/province |
Valencia |
| ZIP/Postal code |
46980 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13945 |
| Series (1) |
| GSE30779 |
Genomic and transcriptomic analysis of aroma synthesis in two hybrids between Saccharomyces cerevisiae and S. kudriavzevii in winemaking conditions |
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