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Sample GSM212411 Query DataSets for GSM212411
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent-Replicate COX7
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent-Replicate COX7
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent-Replicate COX7
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 -5.3219 51 53 17 48 50 15 6 144 148 34 83 85 13 98 0.025 0.047 0.228 0.215 3.088 0.059 0 0.025
2 -4.5735 54 56 18 46 48 13 15 181 186 40 81 82 12 100 0.042 0.057 0.158 0.133 3.162 0.076 0 0.042
3 -5.3808 50 51 14 46 48 15 5 105 107 23 80 82 13 69 0.024 0.045 0.286 0.345 4.051 0.047 0 0.024
4 -8.9658 54 54 17 46 49 15 9 2282 2466 732 80 81 16 100 0.002 0.002 0.006 0.006 2.266 0.002 0 0.002
5 49 50 15 46 48 15 4 200 206 43 79 79 9 100 0.000 0.007 0.097 0.077 2.954 0.032 0 0.000
6 48 50 15 47 49 15 3 75 75 12 80 80 9 29 -0.083 0.083 1.127 1.067 3.521 30.882 -50 -0.083
7 46 48 15 47 49 14 4 150 153 45 78 78 9 99 -0.034 -0.011 0.158 0.148 3.146 0.001 0 -0.034
8 -6.1584 54 56 16 46 48 14 12 421 429 110 78 79 9 100 0.014 0.019 0.041 0.038 2.938 0.024 0 0.014
9 48 50 16 47 49 16 4 70 70 11 79 79 9 17 -0.143 0.143 1.000 0.986 3.757 128.431 -50 -0.143
10 47 50 16 47 49 15 5 106 110 25 77 78 9 90 -0.047 0.021 0.500 0.428 3.587 0.118 0 -0.047
11 48 53 19 46 48 15 8 74 76 10 77 78 10 17 -0.091 0.308 1.546 1.644 2.823 -172.369 0 -0.091
12 -5.9658 50 50 13 45 48 14 1 126 128 25 77 78 9 98 0.016 0.015 0.212 0.233 3.154 0.014 0 0.016
13 -6.1584 50 51 17 47 49 13 6 137 138 30 78 78 9 99 0.014 0.027 0.200 0.199 2.592 0.014 0 0.014
14 48 49 15 50 51 13 7 87 89 16 78 80 12 46 -0.042 0.000 0.830 0.684 3.974 0.397 0 -0.042
15 -7.6439 53 53 15 50 51 15 2 820 867 298 79 81 13 100 0.005 0.005 0.013 0.013 2.588 0.002 0 0.005
16 49 51 15 49 51 15 5 107 112 25 79 80 12 86 0.000 0.041 0.366 0.357 3.535 0.031 0 0.000
17 49 51 15 49 50 14 5 67 68 12 79 80 19 0 0.000 0.400 0.689 0.799 3.514 34.402 -50 0.000
18 48 51 28 48 50 15 3 64 67 16 79 80 21 0 -1.000 0.500 0.625 0.664 3.521 0.470 -50 -1.000
19 -0.5166 2009 2138 786 49 51 14 100 2868 2905 1041 78 80 25 100 0.699 0.735 0.721 0.736 1.243 0.725 -100 0.699
20 -0.5002 1899 1944 653 50 52 16 100 2679 2714 953 79 79 9 100 0.707 0.715 0.717 0.729 1.241 0.698 -100 0.707

Total number of rows: 6979

Table truncated, full table size 667 Kbytes.




Supplementary file Size Download File type/resource
GSM212411.tif.gz 7.5 Mb (ftp)(http) TIFF
Processed data included within Sample table
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