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Sample GSM212008 Query DataSets for GSM212008
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent ETR1
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent ETR1
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent ETR1
Extracted molecule total RNA
Extraction protocol Cells were collected as quiescent or non-quiescent cell fractions. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixed 1:1.
Label Cy5
Label protocol RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.
 
Channel 2
Source name Yeast stationary phase and Exponental mix 1:1
Organism Saccharomyces cerevisiae
Characteristics As a control Yeast stationary phase and Exponental mix 1:1
Extracted molecule total RNA
Extraction protocol Cells were collected as quiescent or non-quiescent cell fractions. All RNA isolation was accomplished with a modified Gentra protocol followed by Qiagen RNeasy Mini Kit reagents. As a control, exponential and stationary phase RNA were mixed 1:1.
Label Cy3
Label protocol RNA (20 µg) was annealed with 2 µg oligo dT, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.25 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP. RNA was degraded using RNase H and RNase A.
 
 
Hybridization protocol The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and re-suspended in 30 µl of the hybridization solution.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were normalized to exogonus controls.
Description Yeast
Data processing After background correction based on negative controls and removal of flaged valuse, data was normalized to Arabidopsis thaliana controls.
 
Submission date Jul 20, 2007
Last update date Aug 14, 2011
Contact name Sushmita Roy
E-mail(s) sroy@cs.unm.edu
Phone 5052779340
Organization name Biology, University of New Mexico
Street address
City Albuquerque
State/province NM
ZIP/Postal code 87106
Country USA
 
Platform ID GPL5627
Series (2)
GSE8560 Mutant1
GSE8624 Quiescent and non-quiescent deletion-mutant strains

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE, test/reference, normalized to Arabidopsis thaliana controls
F635 Median
F635 Mean
F635 SD
B635 Median
B635 Mean
B635 SD
% > B635+2SD
F532 Median
F532 Mean
F532 SD
B532 Median
B532 Mean
B532 SD
% > B532+2SD
Ratio of Medians (635/532)
Ratio of Means (635/532)
Median of Ratios (635/532)
Mean of Ratios (635/532)
Ratios SD (635/532)
Rgn Ratio (635/532)
Flags
PRE_VALUE value

Data table
ID_REF VALUE F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+2SD F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+2SD Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Flags PRE_VALUE
1 -0.7084 139 145 55 53 55 19 85 207 221 70 78 80 19 99 0.612 0.596 0.633 0.582 2.090 0.640 0 0.612
2 -0.4719 191 195 72 53 55 18 97 257 262 82 76 77 15 96 0.721 0.723 0.713 0.749 2.008 0.750 0 0.721
3 -2.3076 70 70 19 53 56 21 15 164 171 63 78 84 50 51 0.202 0.189 0.287 0.245 3.072 0.188 0 0.202
4 -3.1456 396 427 167 50 53 19 100 3137 3486 1353 77 79 18 100 0.113 0.110 0.114 0.108 1.390 0.099 0 0.113
5 -2.5564 98 103 38 50 53 16 71 349 369 95 75 76 12 100 0.170 0.175 0.179 0.156 2.343 0.150 0 0.170
6 -2.2243 61 64 20 50 52 16 20 116 117 22 74 75 10 92 0.214 0.263 0.500 0.409 3.314 0.559 0 0.214
7 -2.0710 78 83 31 50 53 17 42 182 190 50 75 76 10 100 0.238 0.262 0.265 0.241 2.936 0.253 0 0.238
8 -1.8625 156 160 57 51 54 17 93 449 497 162 75 76 11 100 0.275 0.254 0.249 0.235 1.627 0.230 0 0.275
9 -1.3219 71 78 29 51 54 18 31 115 113 17 77 78 11 96 0.400 0.547 0.786 0.807 3.113 1.603 0 0.400
10 -0.9434 88 93 36 52 54 16 60 135 140 32 75 76 11 100 0.520 0.550 0.683 0.651 2.270 0.621 0 0.520
11 -1.2481 65 67 21 52 54 17 18 98 99 18 74 75 11 80 0.421 0.462 0.840 0.882 3.539 1.869 0 0.421
12 -1.8573 73 74 23 51 56 35 3 147 156 36 75 78 29 89 0.276 0.260 0.361 0.305 2.339 0.263 0 0.276
13 -1.7760 70 73 25 52 56 26 13 132 141 33 76 79 28 77 0.292 0.296 0.393 0.315 3.267 0.275 0 0.292
14 -1.1329 75 78 25 53 55 17 35 117 116 20 77 80 22 70 0.456 0.518 0.742 0.645 2.839 0.386 0 0.456
15 -1.1016 264 285 120 51 54 17 99 521 573 245 76 78 18 95 0.466 0.460 0.461 0.489 2.319 0.419 0 0.466
16 -1.6171 79 81 27 53 55 17 40 152 150 29 76 77 10 100 0.326 0.356 0.395 0.358 2.607 0.366 0 0.326
17 -0.5842 63 65 19 53 55 18 18 81 83 14 77 83 95 0 0.667 0.696 1.294 1.492 3.824 4.803 0 0.667
18 -0.3921 65 67 29 53 54 16 18 81 83 17 76 76 10 51 0.762 0.783 1.333 1.351 4.097 19.336 0 0.762
19 -5.6439 80 84 27 55 56 17 43 1582 1801 776 77 82 51 100 0.020 0.020 0.019 0.016 2.750 0.014 -100 0.020
20 -5.6439 73 78 28 53 55 17 36 1267 1404 417 77 82 54 100 0.020 0.022 0.019 0.017 2.503 0.017 -100 0.020

Total number of rows: 6979

Table truncated, full table size 696 Kbytes.




Supplementary file Size Download File type/resource
GSM212008.tif.gz 8.7 Mb (ftp)(http) TIFF
Processed data included within Sample table
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