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Sample GSM212373 Query DataSets for GSM212373
Status Public on Dec 27, 2007
Title BY4742 Quiescent-Replicate SPG1
Sample type RNA
 
Channel 1
Source name BY4742 Quiescent-Replicate SPG1
Organism Saccharomyces cerevisiae
Characteristics BY4742 Quiescent-Replicate SPG1
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 -1.2042 93 97 32 46 48 15 73 169 182 54 80 82 21 98 0.434 0.420 0.555 0.510 2.053 0.452 0 0.434
2 0.0101 188 194 68 45 47 15 99 203 211 62 80 84 28 97 1.007 0.993 1.088 1.144 1.887 1.129 0 1.007
3 -1.6171 61 62 19 45 47 14 23 106 107 28 80 81 11 75 0.326 0.341 0.568 0.645 3.846 0.458 0 0.326
4 -3.1203 277 313 131 45 47 15 100 2058 2364 1031 80 80 11 100 0.115 0.116 0.112 0.116 1.556 0.108 0 0.115
5 -0.1993 175 187 73 46 48 15 97 210 224 80 79 80 13 100 0.871 0.870 0.973 0.973 1.793 1.019 0 0.871
6 0.0000 61 65 24 49 51 16 19 77 80 18 80 82 13 23 1.000 1.059 0.889 1.051 3.310 58.651 0 1.000
7 -0.1714 126 140 61 47 49 16 85 152 160 43 80 81 11 99 0.888 0.959 1.061 1.052 2.685 1.344 0 0.888
8 0.7545 607 685 252 47 49 15 100 395 415 129 79 80 10 100 1.687 1.813 1.834 1.901 1.351 2.108 0 1.687
9 0.0000 69 73 26 47 49 15 37 85 86 19 80 81 11 48 1.000 1.130 2.071 1.659 4.072 6.048 0 1.000
10 0.2388 119 125 49 48 51 16 82 124 128 34 79 81 14 90 1.180 1.200 1.640 1.613 2.392 1.956 0 1.180
11 0.3785 73 77 28 47 50 15 39 83 85 18 79 82 16 23 1.300 1.364 2.364 2.415 3.970 7.397 0 1.300
12 -0.9051 94 97 37 47 50 15 68 151 154 44 80 83 17 94 0.534 0.549 0.741 0.663 2.865 0.719 0 0.534
13 -0.4461 105 111 42 46 49 15 76 142 151 40 78 79 14 97 0.734 0.727 0.864 0.839 2.102 1.009 0 0.734
14 0.5380 108 111 41 46 49 15 79 105 107 28 78 79 12 72 1.452 1.455 1.793 1.899 2.722 2.542 0 1.452
15 -1.5821 352 374 133 47 49 14 100 976 1089 368 77 78 10 100 0.334 0.319 0.322 0.317 1.367 0.317 0 0.334
16 -0.5585 102 105 44 47 48 14 72 144 150 48 76 77 23 79 0.679 0.667 0.794 0.813 2.949 0.781 0 0.679
17 -1.5864 51 54 18 47 49 15 8 75 76 14 78 79 19 3 0.333 0.538 1.000 1.099 3.842 -164.516 -50 0.333
18 -0.2636 57 63 26 49 51 16 26 75 78 18 80 82 14 20 0.833 1.067 1.065 1.093 3.153 3.111 0 0.833
19 -9.9658 54 59 20 47 49 15 19 5174 5739 2676 81 84 15 100 0.001 0.002 0.003 0.003 3.107 0.002 -100 0.001
20 -8.3808 58 60 18 48 50 15 12 4349 4637 1715 84 85 12 100 0.003 0.003 0.003 0.003 2.753 0.002 -100 0.003

Total number of rows: 6979

Table truncated, full table size 692 Kbytes.




Supplementary file Size Download File type/resource
GSM212373.tif.gz 8.1 Mb (ftp)(http) TIFF
Processed data included within Sample table
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