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Sample GSM630236 Query DataSets for GSM630236
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

Data table header descriptions
ID_REF
VALUE normalized log2 ratio test/ref
Signal Norm_Cy5
Signal Norm_Cy3

Data table
ID_REF VALUE Signal Norm_Cy5 Signal Norm_Cy3
1 -0.380018765075587 4277.36 5566.38
2 0.287561647654669 261.252 214.04
3 -0.108077134894834 471.277 507.938
4 0.102276820197422 46.3556 43.1831
5 0.0649829599380952 432.528 413.478
6 -0.0682856199792766 111.636 117.047
7 0.0910905158866102 439.504 412.612
8 -0.049321645169106 857.231 887.044
9 0.0016250173619712 302.023 301.683
10 -0.0174580786678694 55.6736 56.3514
11 0.138795880027191 4121.1 3743.1
12 0.0496994054437736 47.1467 45.5502
13 -0.16231657196256 115.592 129.357
14 -0.0188007269580431 144.622 146.519
15 -0.065081449426997 2078.06 2173.95
16 0.013049106455667 64.2147 63.6365
17 0.0378612966268249 46.3399 45.1396
18 -0.354340917281943 4874.58 6231.67
19 0.0157629135829682 10803.8 10686.4
20 -0.0630396251673694 868.543 907.336

Total number of rows: 15552

Table truncated, full table size 609 Kbytes.




Supplementary file Size Download File type/resource
GSM630236.txt.gz 680.1 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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