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Sample GSM211993 Query DataSets for GSM211993
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent ATG8
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent ATG8
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent ATG8
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 -5.7179 64 88 76 66 70 28 13 126 148 81 105 109 30 41 0.019 0.329 0.969 1.035 3.459 0.751 -50 0.019
2 -1.6758 94 145 118 70 79 45 32 171 231 128 102 109 41 60 0.313 0.516 0.720 0.596 3.171 0.831 -50 0.313
3 -1.4779 115 168 127 78 84 44 38 217 255 124 105 116 45 67 0.359 0.574 0.662 0.583 2.893 0.875 -50 0.359
4 -1.4112 113 1033 3098 80 151 776 8 205 875 2460 107 136 383 7 0.376 1.208 0.578 0.517 3.891 1.267 -50 0.376
5 -0.3603 345 2309 3059 75 151 778 33 434 2128 2616 101 132 387 39 0.779 1.092 1.148 0.919 2.622 1.176 -50 0.779
6 -1.0291 113 252 263 68 80 74 33 174 255 176 97 111 71 41 0.490 1.033 1.155 0.927 3.265 1.526 -50 0.490
7 -1.5187 85 107 73 69 77 34 20 135 160 87 102 115 45 32 0.349 0.500 0.850 0.913 3.629 0.751 -50 0.349
8 -0.5374 145 238 288 71 84 61 34 191 310 334 110 127 70 46 0.689 0.735 0.861 0.854 3.248 0.801 -50 0.689
9 -0.6016 171 289 261 69 80 59 48 236 402 338 102 122 69 53 0.659 0.685 0.778 0.771 2.344 0.746 -50 0.659
10 -0.5479 89 120 101 64 71 34 25 110 136 81 87 99 41 25 0.684 0.891 1.050 0.963 3.471 1.311 -50 0.684
11 -0.2863 113 142 97 60 65 30 44 133 148 72 82 87 25 54 0.820 1.039 1.253 1.189 2.806 1.482 -50 0.820
12 -1.1779 86 127 100 58 63 26 36 124 161 126 84 91 33 42 0.442 0.719 0.989 1.022 3.177 0.716 -50 0.442
13 -0.6326 103 138 101 58 63 26 45 134 208 150 84 89 27 51 0.645 0.551 0.727 0.748 2.911 0.609 -50 0.645
14 -0.5842 97 121 85 57 61 24 42 123 172 100 83 86 18 54 0.667 0.580 0.732 0.773 2.807 0.707 -50 0.667
15 -0.5374 105 211 295 57 64 52 28 133 542 1297 89 96 102 11 0.689 0.315 1.038 1.033 3.227 0.210 -50 0.689
16 -1.7466 120 259 258 58 65 51 45 263 907 1026 96 102 100 50 0.298 0.235 0.308 0.329 3.072 0.219 -50 0.298
17 -1.5864 78 94 51 59 64 26 26 117 176 108 106 110 29 44 0.333 0.298 0.494 0.487 3.256 0.330 -50 0.333
18 -2.4739 72 77 29 60 65 27 7 122 127 38 121 129 40 21 0.180 0.255 0.906 0.764 5.307 -0.148 -50 0.180
19 -2.8678 76 122 136 60 67 35 15 167 4105 11996 139 191 1079 11 0.137 0.015 0.229 0.182 8.276 0.009 -100 0.137
20 -4.4112 112 159 118 59 67 36 45 1115 8368 9903 137 217 1194 48 0.047 0.012 0.015 0.022 5.152 0.009 -100 0.047

Total number of rows: 6979

Table truncated, full table size 710 Kbytes.




Supplementary file Size Download File type/resource
GSM211993.tif.gz 9.2 Mb (ftp)(http) TIFF
Processed data included within Sample table
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