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Sample GSM132691 Query DataSets for GSM132691
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 24 hours, replicate 2
Sample type RNA
 
Channel 1
Source name Oryza sativa suspension cells under suc starvation for 24 hours
Organism Oryza sativa
Characteristics Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 24 hours
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose for 24 hours.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted by use of the TripureTM Kit according to the manufacturer's manual (Genesis Biotech, Taipei, Taiwan). mRNA from control and Suc-starved cells were purified from the respective 200 ug total RNA by use of Oligotex mRNA Mini Kit (Qiagen, Valencia, CA, USA).
Label Cy5
Label protocol Total RNA extraction and mRNA purified from Suc-starved cells and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm
 
Channel 2
Source name Oryza sativa suspension cells control treatment for 24 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 24 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% sucrose for 24 hours.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted by use of the TripureTM Kit according to the manufacturer's manual (Genesis Biotech, Taipei, Taiwan). mRNA from control and Suc-starved cells were purified from the respective 200 ug total RNA by use of Oligotex mRNA Mini Kit (Qiagen, Valencia, CA, USA).
Label Cy3
Label protocol Total RNA extraction and mRNA purified from control cells and the labeling of fluorescent cDNA probes were performed by the methods described in http://www.botany.sinica.edu.tw/microarray/protocols.htm
 
 
Scan protocol The hybridization signals for each DNA element were detected with the use of Axon GenePix 4000B and analyzed with use of GenePix 4.0 (Axon Instruments, Inc., Union City, CA, USA).
Description Rice suspension cells under suc starvation for 24 hours, replecate 2
Data processing After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.
 
Submission date Aug 30, 2006
Last update date Sep 19, 2006
Contact name Huei-Jing Wang
E-mail(s) nkk388@gate.sinica.edu.tw
Organization name Academia sinica
Department Inst of plant and microbial biology
Lab 126
Street address Academia Road, 128, Sec.2, Nankang
City Taipei
State/province Taipei
ZIP/Postal code 11529
Country Taiwan
 
Platform ID GPL892
Series (1)
GSE5853 Transcriptomic adaptations in rice suspension cells under sucrose starvation

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
CH1_Median Channel 1 median intensity
CH1_MEAN Channel 1 mean intensity
CH1_SD Channel 1 mean standard deviation
CH1_BKD_Median
CH1_BKD_MEAN
CH1_BKD_SD
% > CH1_BKD_+1SD Percent of feature pixels that were greater than one standard deviations of the background over the background signal
% > CH1_BKD_+2SD Percent of feature pixels that were greater than two standard deviations of the background over the background signal
CH2_Median Channel 2 median intensity
CH2_MEAN Channel 2 mean intensity
CH2_SD Channel 2 mean standard deviation
CH2_BKD_Median
CH2_BKD_MEAN
CH2_BKD_SD
% > CH2_BKD_+1SD Percent of feature pixels that were greater than one standard deviations of the background over the background signal
% > CH2_BKD_+2SD Percent of feature pixels that were greater than two standard deviations of the background over the background signal
Ratio_of_Medians Unnormalized, untransformed ratio of medians
Ratio_of_Means Unnormalized, untransformed ratio of means
Log_Ratio unnormalized log2 ratio of means defined as CH1 divided by CH2
CH1_Median - CH1_BKD_ Channel 1 median signal
CH2_Median - CH2_BKD_ Channel 2 median signal
CH1_Mean - CH1_BKD_ Channel 1 mean signal
CH2_Mean - CH2_BKD_ Channel 2 mean signal
Flags 0 denotes satisfactory features, while <0 denotes features that did not meet
UNF_VALUE lowess Normalized log2 ratio of means defined as CH1 divided by CH2

Data table
ID_REF VALUE CH1_Median CH1_MEAN CH1_SD CH1_BKD_Median CH1_BKD_MEAN CH1_BKD_SD % > CH1_BKD_+1SD % > CH1_BKD_+2SD CH2_Median CH2_MEAN CH2_SD CH2_BKD_Median CH2_BKD_MEAN CH2_BKD_SD % > CH2_BKD_+1SD % > CH2_BKD_+2SD Ratio_of_Medians Ratio_of_Means Log_Ratio CH1_Median - CH1_BKD_ CH2_Median - CH2_BKD_ CH1_Mean - CH1_BKD_ CH2_Mean - CH2_BKD_ Flags UNF_VALUE
7227 -0.3965159 5025 4806 997 76 82 38 100 100 7206 6815 2135 116 119 44 99 96 0.698 0.706 -0.519 4949 7090 4730 6699 0 -0.3965159
21137 0.06973535 1564 1464 466 71 78 42 98 97 1702 1609 549 110 113 41 96 95 0.938 0.929 -0.093 1493 1592 1393 1499 0 0.06973535
8416 0.16564511 3207 2972 1119 77 84 44 96 95 2983 2771 951 110 114 42 97 97 1.089 1.088 0.124 3130 2873 2895 2661 0 0.16564511
10242 -0.84239155 773 720 299 79 85 41 90 89 2040 2010 343 115 127 217 100 100 0.361 0.338 -1.472 694 1925 641 1895 0 -0.84239155
2905 -0.6886851 309 318 148 72 78 38 93 86 744 729 220 112 116 42 97 96 0.375 0.399 -1.415 237 632 246 617 0 -0.6886851
12687 -1.247401 6399 5883 2178 75 82 40 96 95 20654 20022 5296 113 115 42 100 100 0.308 0.292 -1.7 6324 20541 5808 19909 0 -1.247401
14466 0.16196708 96 110 55 82 85 39 34 18 206 227 76 123 141 66 71 15 0.169 0.269 -2.568 14 83 28 104 0 0.16196708
12682 0.59519565 4249 4233 867 83 88 41 100 100 2575 2480 689 114 117 39 97 96 1.693 1.754 0.759 4166 2461 4150 2366 0 0.59519565
1164 -0.26634613 7578 7347 2751 69 77 40 99 97 9339 9461 3327 116 121 45 100 99 0.814 0.779 -0.297 7509 9223 7278 9345 0 -0.26634613
13497 -0.15817888 346 336 153 74 83 40 91 85 557 551 164 116 119 43 99 97 0.617 0.602 -0.697 272 441 262 435 0 -0.15817888
6298 -0.11848863 2488 2312 847 77 82 40 97 95 3082 2945 897 114 119 42 99 97 0.812 0.789 -0.3 2411 2968 2235 2831 0 -0.11848863
1338 -0.6672014 1390 1302 491 69 76 40 94 94 2965 2860 1579 103 108 40 97 97 0.462 0.447 -1.115 1321 2862 1233 2757 0 -0.6672014
2074 0.038075496 871 850 363 73 79 41 95 94 1056 1030 378 112 115 45 96 95 0.845 0.846 -0.242 798 944 777 918 0 0.038075496
3639 0.8169012 23119 22883 3282 76 81 39 100 100 9560 8650 3248 112 116 42 95 92 2.439 2.671 1.286 23043 9448 22807 8538 0 0.8169012
17157 -0.99730176 221 231 101 73 80 40 90 77 701 697 210 117 119 42 97 97 0.253 0.272 -1.98 148 584 158 580 0 -0.99730176
16146 0.23372759 1875 1804 527 77 83 41 100 100 1713 1572 614 108 114 40 91 90 1.12 1.18 0.164 1798 1605 1727 1464 0 0.23372759
21197 -0.6100194 225 239 117 68 74 39 86 79 546 573 173 112 115 44 99 98 0.362 0.371 -1.467 157 434 171 461 0 -0.6100194
21104 0.051969536 178 188 92 68 74 38 81 67 300 296 85 108 113 43 95 89 0.573 0.638 -0.804 110 192 120 188 0 0.051969536
16066 -0.688665 174 172 79 77 81 41 71 54 439 447 125 116 119 41 100 98 0.3 0.287 -1.735 97 323 95 331 0 -0.688665
20106 -1.1540947 1244 1183 496 68 77 42 94 92 4219 4107 1002 110 114 45 100 100 0.286 0.279 -1.805 1176 4109 1115 3997 0 -1.1540947

Total number of rows: 21495

Table truncated, full table size 2604 Kbytes.




Supplementary data files not provided
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