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Sample GSM212405 Query DataSets for GSM212405
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent-Replicate ATP2
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent-Replicate ATP2
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent-Replicate ATP2
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 -4.7959 57 59 20 53 56 18 8 167 179 54 91 93 13 95 0.036 0.052 0.152 0.172 3.822 0.046 0 0.036
2 -3.9885 62 65 21 55 58 18 10 209 213 50 93 95 15 100 0.063 0.085 0.176 0.142 2.834 0.062 0 0.063
3 53 57 19 57 59 19 5 132 141 37 95 99 19 71 -0.020 0.052 0.379 0.369 3.137 0.010 0 -0.020
4 -5.2109 119 126 47 56 58 19 71 2530 2764 1064 98 101 18 100 0.027 0.027 0.026 0.022 2.201 0.024 0 0.027
5 -6.0589 57 60 19 56 58 20 3 285 299 96 97 98 14 100 0.015 0.028 0.082 0.066 3.200 0.010 0 0.015
6 -2.6990 58 60 20 54 57 18 8 109 113 26 94 95 13 48 0.154 0.200 0.823 0.717 3.243 0.468 0 0.154
7 -4.5395 58 59 17 54 56 17 6 176 181 54 94 95 13 96 0.043 0.051 0.151 0.161 3.466 0.028 0 0.043
8 -4.9214 65 67 23 54 56 17 20 412 444 160 94 96 15 100 0.033 0.036 0.072 0.062 2.316 0.029 0 0.033
9 -1.5228 62 64 19 56 58 18 7 106 110 22 96 98 16 38 0.348 0.370 0.798 0.652 4.250 0.356 0 0.348
10 -4.1844 57 58 19 57 59 18 8 138 145 36 94 96 13 85 0.055 0.065 0.284 0.266 3.241 -0.015 0 0.055
11 -1.3040 71 108 126 58 60 18 31 125 181 181 98 101 18 71 0.405 0.551 0.667 0.571 3.330 0.676 0 0.405
12 51 56 18 54 57 17 5 147 152 39 94 96 16 85 -0.047 0.029 0.250 0.259 3.133 -0.003 0 -0.047
13 -3.8160 59 63 22 55 58 20 5 153 156 44 94 96 16 87 0.071 0.123 0.282 0.294 3.893 0.085 0 0.071
14 -3.1203 57 57 17 55 57 20 2 109 113 25 95 96 14 46 0.115 0.100 0.632 0.624 4.115 0.468 0 0.115
15 -5.7959 66 69 25 55 57 17 16 750 821 319 95 96 12 100 0.018 0.020 0.031 0.024 2.947 0.015 0 0.018
16 -3.2515 60 62 18 54 56 17 7 140 146 33 93 93 12 92 0.105 0.127 0.260 0.286 3.080 0.108 0 0.105
17 -1.5864 56 59 17 55 56 17 5 89 89 14 95 95 18 2 0.333 0.833 0.756 0.857 4.293 53.191 -50 0.333
18 -1.5864 57 59 19 55 57 16 9 92 92 14 95 95 11 16 0.333 0.556 1.455 1.378 4.862 10.273 -50 0.333
19 -1.1078 1795 1774 780 55 58 17 100 3832 4115 1697 95 96 12 100 0.464 0.427 0.432 0.408 1.515 0.421 -100 0.464
20 -1.1976 1320 1410 572 56 61 24 100 2988 3114 1346 102 108 35 100 0.436 0.447 0.452 0.454 1.396 0.421 -100 0.436

Total number of rows: 6979

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM212405.tif.gz 9.0 Mb (ftp)(http) TIFF
Processed data included within Sample table
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