|
| Status |
Public on Dec 09, 2010 |
| Title |
wt-ic003-b |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wt
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain (or line): BY4742
genotype/variation: 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 (or line): BY4742
genotype/variation: 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
Features were extracted using Imagene software from Biodiscovery.
|
| Data processing |
genes, no bg corr, dye corr: as genes, no bg corr, but followed by gene-specific dye bias correction. Identical to genes, no bg corr if the dye bias correction is 0.0, which is the default. So far (jan 2008), we have only dye-bias corrections for yeast.
limma: A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth. The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.
|
| |
|
| Submission date |
Nov 29, 2010 |
| Last update date |
Jun 06, 2013 |
| 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) |
| GSE25644 |
Expression profiling of yeast kinase and phosphatase knockouts |
| GSE42215 |
yeast wt pool |
| GSE45115 |
Expression profiling of 376 wildtypes to assess day-to-day variance |
|
