|
| Status |
Public on Jun 18, 2012 |
| Title |
wt-ea021-1-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 (4)
|
| GSE33097 |
Deletion mutant analysis of established glucose signaling and metabolic pathway members in Saccharomyces cerevisiae |
| GSE33099 |
Glucose signaling |
| GSE42215 |
yeast wt pool |
| GSE45115 |
Expression profiling of 376 wildtypes to assess day-to-day variance |
|
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