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Sample GSM630520 Query DataSets for GSM630520
Status Public on Dec 09, 2010
Title ygk3-del-2-b
Sample type RNA
 
Channel 1
Source name ygk3-del
Organism Saccharomyces cerevisiae
Characteristics strain (or line): BY4742
genotype/variation: ygk3-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 0.278241575696141 22408.2 18477.7
2 -0.0359283107703219 205.74 210.928
3 0.0601302954633797 607.116 582.332
4 -0.268733314787916 49.7432 59.9281
5 -0.00227429202278316 559.055 559.937
6 0.153844611697715 272.284 244.743
7 0.0337487603639338 550.919 538.181
8 -0.0978047854717982 1356.64 1451.8
9 -0.0167999388659385 388.973 393.529
10 -0.0400440673383562 68.4592 70.386
11 0.208858062102868 5283.57 4571.46
12 -0.0673037099248168 52.5581 55.0681
13 0.213428472231666 369.611 318.784
14 -0.0206082631425952 167.442 169.851
15 -0.00607380549787708 3420.31 3434.74
16 0.0418996116935388 74.3583 72.2298
17 -0.0884635726655844 51.8302 55.1078
18 0.534414699118948 27267.3 18826.4
19 0.0385906076699085 10915.2 10627.1
20 0.0287198004920772 988.929 969.437

Total number of rows: 15552

Table truncated, full table size 607 Kbytes.




Supplementary file Size Download File type/resource
GSM630520.txt.gz 689.2 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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