|
| Status |
Public on Jul 25, 2008 |
| Title |
S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 15ºC rep3 |
| Sample type |
RNA |
| |
|
| Source name |
S. cerevisiae CEN.PK113-7D continuous culture D=0.05 at 15ºC
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Strain: S. cerevisiae CEN.PK113-7D
Growth conditions: Steady state chemostat cultures, N-limited, anaerobic at D=0.05h-1, 15ºC in Minimal Media supplemented with anaerobic factors.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples for RNA isolation were taken by rapidly sampling 20 mL of culture into a tube with 35-40 mL of crushed ice, decreasing sample temperature to below 2ºC in less than 10 seconds. Cells were pelleted (4500 RPM at 0ºC for 2 minutes), instantly frozen in liquid nitrogen and stored at -80ºC until further use. Total RNA was extracted using FastRNA Pro RED kit (QBiogene, Inc, USA) according to manufacturer’s instructions after thawing samples on ice. Samples with good RNA integrity and quality, assessed by the RNA 6000 Nano LabChip kit ran on an Agilent 2100 Bioanalyzer, were hybridized.
|
| Label |
Biotin
|
| Label protocol |
mRNA extraction, cDNA synthesis, cRNA synthesis and labeling as well as hybridization to Affymetrix Yeast Genome 2.0 arrays, were performed with the GeneChip one cycle target labeling kit as described in the Affymetrix users’ manual
|
| |
|
| Hybridization protocol |
Affymetrix standard protocol (overnight)
|
| Scan protocol |
Affymetrix standard protocol using Affymetirix Fluidics 400 and Scanner 3000
|
| Description |
Transcriptional response in laboratory and wine strains of S. cerevisiae to growth temperature
|
| Data processing |
Acquisition and primary data analysis of array images was performed using the Affymetrix Microarray suite v5.0 and dChip 2005 software packages. dChip was used to normalize the data. All arrays were globally scaled to a target value of 120 using the invariant set normalization method. Probe summarization was made using only the perfect match (PM) values. From the 10765 transcript features on the Yeast genome 2.0 arrays, a filter was applied to extract 5814 unique S. cerevisiae open reading frames.
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| |
|
| Submission date |
Jul 24, 2008 |
| Last update date |
Jul 24, 2008 |
| Contact name |
Francisco J Pizarro |
| E-mail(s) |
[email protected]
|
| Phone |
+5623544255
|
| Fax |
+5623545803
|
| URL |
http://www.ing.puc.cl/biotec_group
|
| Organization name |
Universidad Catolica de Chile
|
| Department |
Chemical and Bioprocess Engineering
|
| Lab |
Biotechnology
|
| Street address |
Av. Vicuna Mackenna 4860
|
| City |
Santiago |
| ZIP/Postal code |
7820436 |
| Country |
Chile |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE12232 |
Transcriptional response in laboratory and wine strains of S. cerevisiae to growth temperature |
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