|
Status |
Public on Dec 09, 2010 |
Title |
ppq1-del-2-b |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
ppq1-del
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain (or line): BY4742 genotype/variation: ppq1-del
|
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 |
GSE42526 |
Compendium of deletion mutant gene expression profiles, 784 non-responsive mutants [hs1990] |
GSE42528 |
Compendium of deletion mutant gene expression profiles |
|