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Sample GSM211975 Query DataSets for GSM211975
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent YBL048W
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent YBL048W
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent YBL048W
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 50 70 72 47 50 16 13 78 95 57 72 75 17 20 -0.062 0.576 1.167 1.177 3.385 1.129 -50 -0.062
2 -0.5395 73 127 102 46 49 16 45 94 151 94 72 75 19 46 0.688 0.854 1.109 1.049 2.520 1.062 -50 0.688
3 -1.6990 63 103 82 48 50 16 37 101 147 89 73 76 19 50 0.308 0.612 0.908 0.891 2.865 0.870 -50 0.308
4 -3.6990 54 66 44 48 50 16 17 101 359 935 74 85 136 8 0.077 0.051 0.364 0.358 4.645 0.038 -50 0.077
5 -3.5395 64 87 57 46 49 15 37 213 992 1182 74 85 128 41 0.086 0.039 0.062 0.090 4.729 0.038 -50 0.086
6 -2.7179 56 59 22 47 49 15 15 95 129 69 73 76 17 48 0.152 0.119 0.389 0.426 4.265 0.148 -50 0.152
7 50 55 22 47 50 16 8 76 88 35 72 75 18 21 -0.071 0.154 1.000 0.962 3.446 0.438 -50 -0.071
8 -1.6439 59 82 74 47 50 18 21 87 123 92 71 74 20 38 0.320 0.508 0.829 0.814 3.481 0.738 -50 0.320
9 -0.6666 68 103 79 48 50 17 39 89 144 99 71 74 20 42 0.630 0.634 0.836 0.914 2.608 0.752 -50 0.630
10 -1.9051 55 60 25 49 51 16 15 77 84 25 71 73 16 21 0.267 0.409 1.093 1.091 3.577 1.331 -50 0.267
11 -0.6371 60 65 28 49 50 15 23 76 84 27 70 72 15 26 0.643 0.636 1.250 1.341 3.593 1.367 -50 0.643
12 -2.5821 54 58 20 48 50 15 11 80 87 28 70 72 14 32 0.167 0.280 0.822 0.914 3.518 0.491 -50 0.167
13 -2.0000 56 60 22 48 50 14 15 82 90 28 70 72 13 42 0.250 0.321 0.758 0.755 3.706 0.488 -50 0.250
14 -1.8059 57 62 23 48 50 14 19 83 86 21 71 72 14 38 0.286 0.458 1.000 0.873 3.404 1.102 -50 0.286
15 -1.0862 59 71 38 48 50 15 27 79 138 182 71 74 25 12 0.471 0.263 1.032 0.878 4.320 0.133 -50 0.471
16 -2.4035 61 70 34 48 50 15 28 115 214 171 71 74 26 50 0.189 0.125 0.237 0.320 4.096 0.134 -50 0.189
17 -4.3219 52 55 19 47 50 15 9 82 92 29 72 74 15 39 0.050 0.133 0.725 0.690 4.056 0.277 -50 0.050
18 51 54 16 48 50 15 6 74 77 18 73 75 16 12 0.000 0.200 1.200 1.300 3.400 2.480 -50 0.000
19 51 56 24 48 51 18 10 82 733 1663 74 90 212 14 0.000 0.007 0.783 0.362 10.821 0.007 -100 0.000
20 -5.7959 56 59 22 47 50 19 9 346 1409 1507 74 102 278 47 0.018 0.006 0.017 0.059 16.463 0.006 -100 0.018

Total number of rows: 6979

Table truncated, full table size 692 Kbytes.




Supplementary file Size Download File type/resource
GSM211975.tif.gz 8.5 Mb (ftp)(http) TIFF
Processed data included within Sample table
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