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Sample GSM212037 Query DataSets for GSM212037
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent ODC1
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent ODC1
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent ODC1
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 0.8303 95 112 59 71 75 30 30 79 94 47 70 73 18 22 1.778 1.485 2.000 2.107 3.298 1.576 -50 1.778
2 0.9092 140 169 105 74 79 32 54 102 144 82 72 75 16 59 1.878 1.277 1.250 1.574 3.272 1.412 -50 1.878
3 0.3103 125 169 118 75 83 35 45 111 151 86 77 84 26 48 1.240 1.178 1.370 1.401 2.972 1.509 -50 1.240
4 -0.4112 139 376 636 76 86 40 47 162 485 1009 76 86 30 68 0.752 0.738 0.846 0.910 2.714 0.598 -50 0.752
5 -0.0740 178 621 863 76 83 37 60 182 956 1405 71 78 25 65 0.950 0.623 0.772 0.860 3.005 0.559 -50 0.950
6 0.6781 103 141 103 74 80 31 36 86 139 99 70 73 17 44 1.600 1.000 1.079 1.199 3.088 1.018 -50 1.600
7 0.1699 99 107 51 75 80 33 26 93 103 37 72 75 19 41 1.125 1.048 1.242 1.307 3.540 1.773 -50 1.125
8 0.4709 124 161 111 75 79 30 50 105 162 140 72 75 18 55 1.386 0.970 1.083 1.277 3.061 0.746 -50 1.386
9 0.7004 102 164 140 73 77 28 42 85 192 197 69 71 15 43 1.625 0.771 0.880 1.031 3.510 0.711 -50 1.625
10 0.5261 99 113 54 73 76 27 37 86 93 28 68 71 16 41 1.440 1.563 1.800 1.542 3.827 2.800 -50 1.440
11 0.6041 101 116 58 72 77 29 37 86 95 35 69 72 16 41 1.520 1.559 1.662 1.765 3.156 2.700 -50 1.520
12 0.2228 91 99 44 70 76 29 25 85 91 32 69 71 15 37 1.167 1.200 1.738 1.633 3.323 2.091 -50 1.167
13 -0.1001 91 104 50 72 78 34 25 91 108 46 70 74 37 23 0.933 0.872 1.117 1.139 3.968 1.189 -50 0.933
14 0.1570 92 97 42 71 77 34 17 87 99 36 70 73 37 15 1.115 0.895 1.000 1.099 3.718 0.828 -50 1.115
15 -0.0908 94 117 72 69 73 27 33 94 160 205 68 71 15 55 0.939 0.545 1.132 1.078 3.603 0.269 -50 0.939
16 -0.5312 99 141 93 69 74 28 42 113 295 301 69 72 18 52 0.692 0.333 0.388 0.544 4.455 0.247 -50 0.692
17 0.0607 87 91 38 69 74 30 17 84 100 43 69 72 16 38 1.043 0.718 1.075 1.010 3.803 1.059 -50 1.043
18 -0.3076 84 88 31 70 76 32 10 87 93 28 71 79 30 16 0.808 0.781 0.860 0.928 3.394 0.884 -50 0.808
19 -0.5842 77 85 37 70 76 30 12 82 386 930 73 81 30 17 0.667 0.068 0.914 0.614 7.861 0.020 -100 0.667
20 -1.0893 94 104 51 70 76 31 28 127 1188 1297 68 71 16 55 0.470 0.036 0.045 0.107 9.853 0.020 -100 0.470

Total number of rows: 6979

Table truncated, full table size 697 Kbytes.




Supplementary file Size Download File type/resource
GSM212037.tif.gz 8.9 Mb (ftp)(http) TIFF
Processed data included within Sample table
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