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Sample GSM347638 Query DataSets for GSM347638
Status Public on Aug 01, 2009
Title Interplay between HDAC clr3 and HAT gcn5 replicate 2
Sample type RNA
 
Channel 1
Source name Schizosaccharomyces pombe gcn5-clr3- double mutant strain Hu1036 treated with KCl
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: gcn5-clr3- double mutant strain Hu1036
agent: 1M KCl
time: 60min
temperature: 25C
Biomaterial provider Anthony Wright
Treatment protocol Schizosaccharomyces pombe gcn5-clr3- double mutant strain Hu1036 treated with 1M KCl for 60min at 25C.
Growth protocol Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.
Extracted molecule total RNA
Extraction protocol See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).
Label Cy3
Label protocol See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).
 
Channel 2
Source name Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with KCl
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: gcn5 mutant Hu0799
agent: 1M KCl
time: 60min
temperature: 25C
Biomaterial provider Anthony Wright
Treatment protocol Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with 1M KCl for 60min at 25C.
Growth protocol Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.
Extracted molecule total RNA
Extraction protocol See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).
Label Cy5
Label protocol See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).
 
 
Hybridization protocol See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).
Scan protocol Slides were scanned using Bio-rad Vers-Array ChipReader.
Description Expression profile of Schizosaccharomyces pombe gcn5-clr3- double mutant strain was compared to gcn5-strain, both treated with 1M KCl in rich medium at 25C.
Data processing Scanned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.
 
Submission date Dec 03, 2008
Last update date Apr 21, 2009
Contact name Anthony Wright
E-mail(s) yongtao.xue.franzen@ki.se
Organization name Karolinska Institute
Lab Anthony Wright
Street address BlickagÄngen 6
City Huddinge
ZIP/Postal code 141 57
Country Sweden
 
Platform ID GPL3425
Series (1)
GSE13817 Deletion of Clr3 restores expression of a subset of genes in gcn5- mutant cells

Data table header descriptions
ID_REF
VALUE log2 Ratio of the test group compared to the control group
NormCH1 Normalized signal of test group
NormCH2 Normalized signal of control group
Raw test signal Non-normalized signal of test group
Raw test background Non-normalized background of test group
Raw control signal Non-normalized signal of control group
Raw control background Non-normalized background of control group
PRE_VALUE Ratio of the test group compared to the control group

Data table
ID_REF VALUE NormCH1 NormCH2 Raw test signal Raw test background Raw control signal Raw control background PRE_VALUE
1 -0.4958 11791.189 16626.57 15469 172 22301 227 0.7091775
2 -0.4040 633.0942 837.67554 850 166 1238 216 0.7557749
3 0.7364 1624.608 975.1534 2136 178 1367 229 1.6660025
4 0.6941 680.1692 420.39633 924 175 796 298 1.6179237
5 1.9047 23489.01 6273.24 32330.5 158 9327 264 3.7443187
6 0.1625 825.85114 737.8927 1036 132 1274 310 1.1192023
7 0.4461 1030.7804 756.6042 1229 141 1204 236 1.3623773
8 0.9776 611.83905 310.69702 906 132 583 227 1.9692466
9 0.2493 12157.166 10228.192 12294 143 11802 265 1.1885937
10 -0.0067 802.12244 805.8828 1038 142 1113 250 0.99533385
11 -0.7740 1729.8032 2958.0698 2094 126 3861 220 0.5847743
12 48833 149 53997 254
13 -0.1675 403.25146 452.8919 554 132 792 292 0.8903923
14 -0.2964 195.58289 240.18489 321 110 580 291 0.8143014
15 -0.0866 13675.891 14521.812 16239 104 20744 222 0.94174826
16 40742 100 47077 256
17 0.6504 877.70593 559.17773 1049 170 926 274 1.5696368
18 -0.6139 368.8676 564.51215 494 136 838 181 0.65342724
19 0.3035 1151.213 932.8326 1310 148 1330 245 1.2341046
20 1.3013 1055.3358 428.21817 1288 152 720 246 2.4644816

Total number of rows: 11520

Table truncated, full table size 610 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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