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Sample GSM212039 Query DataSets for GSM212039
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent PAI3
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent PAI3
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent PAI3
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 48 74 74 47 50 19 14 78 101 75 70 73 15 18 0.000 0.743 1.000 1.062 4.039 0.865 -50 0.000
2 -0.5023 72 102 76 48 50 19 37 100 159 102 73 77 25 41 0.706 0.581 0.761 0.734 3.133 0.629 -50 0.706
3 -1.7370 60 65 28 48 51 17 22 106 154 92 78 83 28 43 0.300 0.193 0.402 0.422 3.924 0.196 -50 0.300
4 -3.9434 54 57 21 48 51 16 13 159 696 1709 80 90 39 60 0.065 0.014 0.155 0.126 6.674 0.007 -50 0.065
5 -4.6439 55 61 26 47 49 15 21 241 1330 1849 76 85 38 62 0.040 0.010 0.037 0.056 8.386 0.008 -50 0.040
6 -3.8573 50 53 17 47 50 15 7 95 177 143 72 77 22 43 0.069 0.045 0.214 0.260 5.621 0.036 -50 0.069
7 48 52 16 48 50 15 7 95 115 65 73 80 26 33 0.000 0.082 0.583 0.520 4.737 0.043 -50 0.000
8 -3.7370 53 64 39 47 49 16 18 133 224 268 73 81 30 51 0.075 0.101 0.222 0.242 4.383 0.112 -50 0.075
9 -1.6259 60 74 45 48 50 16 29 103 269 287 73 79 30 41 0.324 0.128 0.197 0.278 4.425 0.113 -50 0.324
10 -2.2447 52 58 26 48 50 16 12 85 105 58 72 77 26 23 0.211 0.256 0.400 0.497 3.282 0.240 -50 0.211
11 -1.6897 57 62 26 48 50 15 23 95 120 57 72 78 26 40 0.310 0.259 0.480 0.506 3.424 0.254 -50 0.310
12 -3.0000 51 53 17 47 50 15 9 90 118 84 73 79 29 26 0.125 0.096 0.611 0.565 4.542 0.041 -50 0.125
13 -4.2379 50 53 18 47 49 15 9 104 155 95 74 81 29 46 0.053 0.056 0.208 0.248 4.754 0.045 -50 0.053
14 -2.3219 56 63 30 48 50 15 21 106 135 67 77 82 26 46 0.200 0.217 0.381 0.391 5.031 0.143 -50 0.200
15 -2.0469 63 79 47 48 50 17 31 128 424 829 77 87 91 13 0.242 0.087 0.400 0.334 4.471 0.035 -50 0.242
16 -2.8468 59 67 31 49 51 17 26 145 561 679 76 85 93 41 0.139 0.038 0.084 0.130 6.272 0.035 -50 0.139
17 -3.9434 50 53 17 48 50 14 8 97 133 73 77 82 25 38 0.065 0.075 0.333 0.405 5.913 0.030 -50 0.065
18 -3.7370 51 53 16 48 51 15 6 106 116 40 88 108 60 4 0.075 0.100 0.513 0.479 3.996 0.010 -50 0.075
19 -5.2109 51 59 27 50 52 15 14 177 3114 8299 107 170 1027 12 0.027 0.004 0.076 0.049 10.247 0.002 -100 0.027
20 -4.9214 64 69 26 49 52 16 27 554 5940 6859 93 157 1000 46 0.033 0.004 0.006 0.016 13.143 0.002 -100 0.033

Total number of rows: 6979

Table truncated, full table size 691 Kbytes.




Supplementary file Size Download File type/resource
GSM212039.tif.gz 8.6 Mb (ftp)(http) TIFF
Processed data included within Sample table
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