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Sample GSM392031 Query DataSets for GSM392031
Status Public on Aug 01, 2009
Title Schizosaccharomyces pombe clr3 mutant compared to wt KCl treatment,replicate 2 (slide 3)
Sample type RNA
 
Channel 1
Source name Schizosaccharomyces Pombe clr3 mutant Hu0369 treated with KCl
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: gcn5 mutant Hu0369
agent: 1M KCl
time: 60min
temperature: 25C
Biomaterial provider Anthony Wright and Karl Ekwall's laboratory
Treatment protocol Schizosaccharomyces pombe clr3 mutant Hu0369 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).
 
Channel 2
Source name Schizosaccharomyces pombe wild type strain Fy368 treated with KCl for 60min.
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: wild type strain Fy368
agent: KCl
time: 60min
temperature: 25C
Biomaterial provider Anthony Wright and Karl Ekwall's laboratory
Treatment protocol Schizosaccharomyces pombe wild type strain fy368 treated with 1M KCl for 60min.
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).
 
 
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 Schizosaccharomyces pombe clr3 mutant strain compared to wild type strain, both treated with 1M KCl in rich medium at 25C.
Data processing canned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.
 
Submission date Apr 14, 2009
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 Blickagången 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 of PRE_VALUE
normalized signal Normalized signal intensity of test channel (CH1)
normalized control Normalized signal intensity of control channel (CH2)
raw signal Raw signal intensity of test channel
raw signal background Raw signal background of test channel
raw control Raw singal intensity of control channel
raw control background Raw signal intensity of control channel
PRE_VALUE Ratio of test to control channel

Data table
ID_REF VALUE normalized signal normalized control raw signal raw signal background raw control raw control background PRE_VALUE
1 0.6996 11,032 6,792 20368.424242424244 218.82978723404256 11564.873786407767 173.52083333333334 1.624
2 1.0412 607.4 295.1 1498.235294117647 223.53535353535352 923.6363636363636 173.31914893617022 2.058
3 0.2277 1,581 1,350 2230.529411764706 215.8181818181818 2145.9803921568628 163.52083333333334 1.171
4 0.3550 708.2 553.5 1255.2929292929293 250.04494382022472 934.9803921568628 167.8095238095238 1.279
5 0.5811 13,826 9,245 16444.158415841583 246.68085106382978 11152.257425742575 162.3404255319149 1.496
6 0.2786 818.9 675.2 1447.009900990099 253.53846153846155 983.92 143.125 1.213
7 0.1928 821.5 719 1657.939393939394 238.10638297872342 992.16 154.96226415094338 1.143
8 0.4190 400.7 299.8 688.7450980392157 203.85858585858585 593.2475247524752 168.10638297872342 1.337
9 -0.2619 5,941 7,121 6066.21568627451 203.17117117117118 5304.82 168.625 0.834
10 -0.0218 844.9 857.5 1404.0588235294117 217.30526315789473 1101.8640776699028 170.21848739495798 0.985
11 -0.4719 2,174 3,013 3044.0625 228.6601941747573 2665.223300970874 186.8913043478261 0.721
12 39541.03921568627 260.18947368421055 45626.21212121212 153.44086021505376
13 -0.5995 229.7 347.8 759.9803921568628 238.8490566037736 687.1515151515151 172.752688172043 0.66
14 0.2203 211.5 181.5 571.5294117647059 281.7142857142857 434.5 164.0 1.165
15 0.1776 14,471 12,792 29059.48514851485 283.5959595959596 19748.59405940594 193.2842105263158 1.131
16 39230.33663366337 243.06422018348624 45951.62 196.73469387755102
17 0.9358 1,008 526.8 1142.4752475247524 229.71428571428572 1373.171717171717 173.12765957446808 1.913
18 0.3482 430.4 338.2 762.3137254901961 264.34234234234236 645.6862745098039 176.09174311926606 1.273
19 0.5069 1,392 979.7 1568.2745098039215 229.30434782608697 1468.2549019607843 175.16190476190476 1.421
20 0.5170 1,011 706.3 1148.989898989899 265.2258064516129 1083.7227722772277 173.02173913043478 1.431

Total number of rows: 11520

Table truncated, full table size 1061 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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