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Sample GSM212050 Query DataSets for GSM212050
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent SDH4
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent SDH4
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent SDH4
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 0.3219 61 108 124 56 59 25 17 83 115 88 81 85 27 14 1.250 1.444 1.604 1.790 3.241 1.414 -50 1.250
2 -0.6689 78 152 140 57 62 32 39 114 200 144 82 94 43 41 0.629 0.793 0.929 0.914 3.217 0.943 -50 0.629
3 -1.6215 69 104 79 57 61 25 27 119 186 127 83 93 38 41 0.325 0.449 0.565 0.546 3.004 0.517 -50 0.325
4 -2.3437 69 87 52 55 59 22 28 145 730 1575 82 132 387 14 0.197 0.048 0.230 0.200 4.415 0.025 -50 0.197
5 -3.0469 70 95 59 57 60 22 31 195 1388 2030 82 125 363 31 0.121 0.030 0.050 0.098 6.623 0.024 -50 0.121
6 -1.7760 63 67 25 56 59 19 10 103 170 127 81 87 33 32 0.292 0.121 0.348 0.419 5.621 0.045 -50 0.292
7 -1.5864 61 63 20 57 60 19 7 94 107 42 83 89 31 14 0.333 0.250 0.853 0.672 3.802 0.087 -50 0.333
8 -2.1844 65 76 42 59 62 22 17 120 176 142 85 96 40 34 0.220 0.206 0.394 0.418 4.031 0.218 -50 0.220
9 -0.0786 74 92 52 58 61 21 31 98 197 169 85 94 37 33 0.947 0.305 0.382 0.519 4.603 0.235 -50 0.947
10 -0.5842 66 67 21 59 62 21 8 94 105 40 84 91 29 12 0.667 0.423 1.000 0.921 4.005 0.131 -50 0.667
11 -0.7661 66 69 26 60 62 21 12 96 104 37 85 91 29 12 0.588 0.520 0.900 0.783 3.494 0.191 -50 0.588
12 -1.5864 61 65 22 58 61 19 8 94 98 25 83 86 24 12 0.333 0.474 0.775 0.820 3.818 0.385 -50 0.333
13 -1.6620 62 67 24 58 60 19 13 98 104 29 83 85 18 30 0.316 0.440 0.909 0.871 3.967 0.244 -50 0.316
14 -0.9462 70 72 23 58 61 19 16 106 111 26 84 87 18 35 0.519 0.500 0.792 0.778 3.560 0.420 -50 0.519
15 -0.8288 74 94 57 58 62 23 23 111 147 115 85 91 40 15 0.563 0.559 0.826 0.763 3.448 0.399 -50 0.563
16 -0.6282 78 108 77 58 62 23 33 113 202 167 85 91 38 34 0.647 0.423 0.611 0.614 4.167 0.383 -50 0.647
17 -2.6990 58 63 23 58 60 19 10 92 100 27 83 86 16 28 0.154 0.333 0.871 1.028 4.152 0.524 -50 0.154
18 -1.2210 59 60 19 58 60 19 5 86 90 21 83 87 20 5 0.429 0.364 1.257 1.160 4.294 0.322 -50 0.429
19 -1.1714 60 64 22 59 61 19 10 88 346 649 83 95 115 14 0.444 0.030 1.219 0.697 9.263 0.009 -100 0.444
20 -3.2793 66 71 24 58 63 80 0 176 823 812 82 106 204 48 0.103 0.020 0.033 0.075 10.611 0.010 -100 0.103

Total number of rows: 6979

Table truncated, full table size 695 Kbytes.




Supplementary file Size Download File type/resource
GSM212050.tif.gz 8.6 Mb (ftp)(http) TIFF
Processed data included within Sample table
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