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Sample GSM212432 Query DataSets for GSM212432
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent-Replicate GUT2
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent-Replicate GUT2
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent-Replicate GUT2
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)
GSE8561 Mutant2
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 -0.6016 79 89 35 53 58 28 25 114 118 33 96 99 19 53 0.659 0.822 1.206 1.237 4.093 1.911 0 0.659
2 0.3414 147 156 62 52 58 28 75 148 152 40 93 95 18 85 1.267 1.316 1.883 1.847 2.365 1.985 0 1.267
3 -0.6104 71 75 32 55 59 23 23 102 112 32 91 91 13 55 0.655 0.590 0.900 1.097 2.873 1.601 0 0.655
4 -0.8034 695 722 309 50 54 21 100 1196 1322 571 92 93 14 100 0.573 0.536 0.536 0.548 1.345 0.496 0 0.573
5 -0.2636 122 135 52 50 52 15 88 157 171 51 91 91 11 97 0.833 0.847 1.075 1.028 1.939 1.109 0 0.833
6 -1.7370 55 60 22 50 53 18 9 83 83 16 91 91 12 17 0.300 0.800 1.188 1.154 3.690 -85.507 -50 0.300
7 -1.3548 70 76 32 50 53 17 30 119 125 37 90 91 12 71 0.391 0.462 0.824 0.907 3.534 0.738 0 0.391
8 -0.6758 159 170 64 50 52 16 94 244 257 80 89 90 11 100 0.626 0.641 0.696 0.702 1.883 0.613 0 0.626
9 1.4594 63 68 25 49 51 16 21 77 79 16 86 86 12 9 2.750 2.667 2.333 2.050 3.718 -8.586 0 2.750
10 0.5028 86 93 39 52 55 22 36 97 107 36 88 88 13 49 1.417 1.206 1.364 1.303 3.502 2.066 0 1.417
11 0.8624 72 81 30 52 56 22 31 84 85 18 85 86 14 15 1.818 2.417 0.784 1.109 4.584 -10.676 0 1.818
12 -0.4286 78 85 34 51 53 17 35 108 117 32 89 89 11 70 0.743 0.750 1.124 1.343 3.351 1.357 0 0.743
13 -1.1297 68 72 28 50 53 18 24 108 117 32 90 89 12 71 0.457 0.455 0.875 0.844 3.085 1.109 0 0.457
14 -1.3622 59 63 22 50 53 19 7 91 95 18 88 88 12 40 0.389 0.500 0.893 0.867 3.530 4.314 0 0.389
15 -1.7370 187 209 92 49 53 19 95 523 610 278 87 87 13 100 0.300 0.292 0.307 0.291 1.641 0.265 0 0.300
16 -1.8314 61 68 28 51 54 17 21 105 112 31 89 89 14 55 0.281 0.410 1.060 1.021 3.358 1.222 0 0.281
17 50 54 19 51 53 16 6 75 75 14 89 89 14 3 -1.000 1.000 0.700 0.724 3.720 35.858 -50 -1.000
18 50 53 18 51 54 17 6 78 78 17 92 93 15 6 -0.400 0.200 0.529 0.613 3.809 3.173 -50 -0.400
19 -0.7322 1257 1466 823 51 54 16 100 2076 2523 1396 90 90 13 100 0.602 0.577 0.573 0.554 1.437 0.534 -100 0.602
20 -0.8034 1208 1402 716 52 54 16 100 2091 2471 1267 90 91 13 100 0.573 0.563 0.575 0.562 1.278 0.541 -100 0.573

Total number of rows: 6979

Table truncated, full table size 691 Kbytes.




Supplementary file Size Download File type/resource
GSM212432.tif.gz 8.2 Mb (ftp)(http) TIFF
Processed data included within Sample table
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