|
| Status |
Public on Nov 21, 2013 |
| Title |
S. cerevisiae T73 replicate C, Dye Swap, 12ºC fermentation against 28ºC fermentation. |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
yeast cells from wine fermentation at 12ºC
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Lalvin T73
growth phase: Beginning of exponential phase
|
| Growth protocol |
Wine fermentations in Tempranillo must at 12ºC or 28ºC
|
| 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).
|
| |
|
| Channel 2 |
| Source name |
yeast cells from wine fermentation at 28ºC
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Lalvin T73
growth phase: Beginning of exponential phase
|
| Growth protocol |
Wine fermentations in Tempranillo must at 12ºC or 28ºC
|
| 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).
|
| |
|
| |
| 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
|
| 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 |
Comparative gene expression of S. cerevisiae T73 at 12ºC with respect to 28ºC. Replicate C with Dye Swap.
|
| 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. Genes with a two-fold log2 ratio values were considered to be significantly expressed.
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| |
|
| Submission date |
Nov 20, 2013 |
| Last update date |
Nov 21, 2013 |
| Contact name |
Jordi Tronchoni |
| E-mail(s) |
[email protected]
|
| Organization name |
CSIC
|
| Street address |
Avda. Agustín Escardino, 7
|
| City |
Paterna |
| ZIP/Postal code |
46980 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17965 |
| Series (1) |
| GSE52545 |
Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations |
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