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Sample GSM211994 Query DataSets for GSM211994
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent ATP18
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent ATP18
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent ATP18
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 -0.7370 68 85 57 62 67 28 12 67 81 48 67 70 19 9 0.600 1.053 1.750 1.664 3.765 1.238 -50 0.600
2 0.2534 96 136 125 63 69 31 40 88 140 103 67 71 24 41 1.192 0.910 1.000 1.248 3.129 1.155 -50 1.192
3 0.4761 97 138 103 63 69 29 38 85 142 95 69 73 25 42 1.391 0.913 1.128 1.210 3.462 1.051 -50 1.391
4 -0.5842 95 518 1344 72 95 177 10 107 339 826 73 86 94 8 0.667 1.635 1.064 1.231 3.838 1.657 -50 0.667
5 0.2963 275 1208 1640 77 100 173 40 233 864 1078 75 88 92 48 1.228 1.425 1.393 1.390 2.399 1.521 -50 1.228
6 0.8624 105 157 124 71 82 43 35 84 123 72 72 79 28 39 1.818 1.508 1.597 1.670 2.827 1.905 -50 1.818
7 -0.1250 76 90 47 67 72 27 21 74 83 32 69 71 15 21 0.917 1.190 1.852 2.000 4.041 1.983 -50 0.917
8 -0.1993 92 118 80 67 72 31 32 93 119 77 70 73 21 39 0.871 0.930 1.230 1.467 3.415 1.035 -50 0.871
9 -0.1062 91 131 88 66 71 30 39 90 145 99 70 73 20 42 0.929 0.795 1.002 1.159 2.982 0.867 -50 0.929
10 -0.1062 78 87 39 66 71 28 19 76 81 23 69 72 17 18 0.929 1.158 1.818 1.751 3.738 4.133 -50 0.929
11 0.1699 83 91 42 69 74 31 17 78 83 22 70 74 20 16 1.125 1.238 1.923 1.843 3.356 4.419 -50 1.125
12 -0.0786 83 95 58 70 79 40 9 81 99 94 72 81 49 5 0.947 0.811 1.695 1.537 4.131 0.442 -50 0.947
13 -0.6620 77 89 72 72 80 41 7 81 98 119 74 84 48 2 0.632 0.667 1.894 1.670 3.767 0.430 -50 0.632
14 -0.6620 77 86 40 71 77 33 11 81 87 25 75 81 34 5 0.632 0.840 2.333 1.998 3.715 0.537 -50 0.632
15 0.2485 84 93 43 75 88 64 3 78 114 106 80 112 137 8 1.188 0.538 1.367 1.235 4.266 0.259 -50 1.188
16 -1.3219 93 107 56 74 89 67 5 132 172 106 83 123 144 8 0.400 0.382 0.657 0.704 4.233 0.343 -50 0.400
17 -1.3921 73 85 43 69 76 34 11 83 99 56 75 85 40 11 0.381 0.541 1.143 1.136 3.972 0.644 -50 0.381
18 -0.5146 72 80 35 68 72 29 10 72 74 17 72 76 21 4 0.700 1.250 1.643 1.803 4.581 24.097 -50 0.700
19 -0.8237 78 86 37 70 77 37 8 85 397 865 81 210 384 10 0.565 0.063 0.407 0.359 5.886 0.028 -100 0.565
20 -4.5735 90 100 51 71 79 39 18 652 981 974 94 296 468 47 0.042 0.038 0.057 0.098 8.106 0.030 -100 0.042

Total number of rows: 6979

Table truncated, full table size 697 Kbytes.




Supplementary file Size Download File type/resource
GSM211994.tif.gz 8.9 Mb (ftp)(http) TIFF
Processed data included within Sample table
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