|
Status |
Public on Jun 18, 2012 |
Title |
wt-ea032-b |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
wt
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: BY4742 genetic modification: wt
|
Extracted molecule |
total RNA |
Extraction protocol |
yeast RNA isolation for robotic amplification v1.0
|
Label |
Cy5
|
Label protocol |
robot amplification and labeling v1.0
|
|
|
Channel 2 |
Source name |
refpool
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: BY4742 genetic modification: refpool
|
Extracted molecule |
total RNA |
Extraction protocol |
yeast RNA isolation for robotic amplification v1.0
|
Label |
Cy3
|
Label protocol |
robot amplification and labeling v1.0
|
|
|
|
Hybridization protocol |
Tecan HS4800 hybridization
|
Scan protocol |
scanning of slides using Agilent G256BA Imagene feature extraction
|
Data processing |
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.
|
|
|
Submission date |
Oct 19, 2011 |
Last update date |
Jun 18, 2012 |
Contact name |
Patrick Kemmeren |
Organization name |
UMC Utrecht
|
Department |
Department of Molecular Cancer Research
|
Lab |
Holstege Lab
|
Street address |
Universiteitsweg 100
|
City |
Utrecht |
State/province |
Utrecht |
ZIP/Postal code |
3584 CG |
Country |
Netherlands |
|
|
Platform ID |
GPL11232 |
Series (3) |
GSE33097 |
Deletion mutant analysis of established glucose signaling and metabolic pathway members in Saccharomyces cerevisiae |
GSE33099 |
Glucose signaling |
GSE45115 |
Expression profiling of 376 wildtypes to assess day-to-day variance |
|