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Sample GSM212421 Query DataSets for GSM212421
Status Public on Dec 27, 2007
Title BY4742 Non-Quiescent-Replicate FMP21
Sample type RNA
 
Channel 1
Source name BY4742 Non-Quiescent-Replicate FMP21
Organism Saccharomyces cerevisiae
Characteristics BY4742 Non-Quiescent-Replicate FMP21
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 -2.9771 64 66 23 59 65 94 0 152 155 45 112 113 23 66 0.127 0.149 0.432 0.429 3.063 0.149 0 0.127
2 -2.0116 83 82 25 59 66 106 0 194 199 50 112 114 25 87 0.248 0.229 0.346 0.323 2.997 3.275 0 0.248
3 -4.3808 58 58 18 61 62 20 5 143 144 30 112 114 16 78 0.048 0.048 0.553 0.440 4.375 0.050 0 0.048
4 -4.4422 161 173 74 61 63 20 85 2374 2554 1114 112 114 17 100 0.046 0.048 0.045 0.039 2.101 0.043 0 0.046
5 -3.2243 76 83 32 58 60 20 35 277 282 76 113 113 16 100 0.107 0.139 0.176 0.166 2.655 0.113 0 0.107
6 -1.0770 64 65 26 59 62 20 13 100 104 26 110 110 16 30 0.474 0.435 0.629 0.843 3.271 1.775 0 0.474
7 -3.6439 62 66 22 60 62 20 8 169 173 48 110 111 13 94 0.080 0.120 0.337 0.278 3.803 0.027 0 0.080
8 -4.3511 73 78 27 61 64 20 22 452 485 131 110 111 13 100 0.049 0.057 0.056 0.047 3.203 0.035 0 0.049
9 -2.2653 60 62 19 62 64 20 6 105 105 20 110 111 15 34 0.208 0.292 0.894 0.944 3.288 2.568 -50 0.208
10 -3.3364 62 67 21 64 65 21 11 152 153 38 109 111 19 77 0.099 0.167 0.408 0.453 4.262 0.024 0 0.099
11 -1.6529 62 62 18 62 63 19 5 103 101 16 110 111 14 34 0.318 0.350 1.000 0.951 3.578 8.718 -50 0.318
12 -3.1844 63 66 24 62 65 22 9 154 162 44 110 112 31 60 0.110 0.136 0.333 0.276 3.965 0.095 0 0.110
13 -3.9434 61 63 22 61 64 21 5 174 181 66 109 111 26 76 0.065 0.080 0.238 0.204 4.364 0.025 0 0.065
14 -3.1714 60 73 40 62 65 21 15 126 125 35 111 114 19 53 0.111 0.409 1.134 1.254 3.660 0.937 0 0.111
15 -4.4739 103 107 42 61 64 29 33 1154 1242 390 110 112 19 100 0.045 0.045 0.044 0.037 2.335 0.038 0 0.045
16 -5.3808 57 62 22 60 62 19 10 165 169 50 107 108 17 87 0.024 0.080 0.381 0.398 4.043 0.018 0 0.024
17 -2.0000 58 62 20 61 63 19 7 93 93 23 108 108 15 21 0.250 0.583 0.734 0.717 3.515 1.427 -50 0.250
18 -1.1910 62 66 33 62 64 19 9 97 102 43 111 112 17 16 0.438 0.524 0.714 0.769 3.869 0.655 -50 0.438
19 -2.8468 720 821 373 63 64 19 100 4854 5253 2480 113 115 16 100 0.139 0.148 0.147 0.147 1.471 0.134 -100 0.139
20 -2.8468 882 890 394 62 63 18 100 6051 6371 2654 116 118 17 100 0.139 0.133 0.129 0.128 1.502 0.125 -100 0.139

Total number of rows: 6979

Table truncated, full table size 693 Kbytes.




Supplementary file Size Download File type/resource
GSM212421.tif.gz 8.8 Mb (ftp)(http) TIFF
Processed data included within Sample table

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