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Sample GSM132693 Query DataSets for GSM132693
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 48 hours, replicate 1
Sample type RNA
 
Channel 1
Source name Oryza sativa suspension cells under suc starvation for 48 hours
Organism Oryza sativa
Characteristics Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 48 hours
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose for 48 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 48 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 48 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% sucrose for 48 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 48 hours, replecate 1
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 -0.1806465 4714 4855 1062 62 179 1548 100 98 7156 6925 1859 74 211 1961 94 92 0.657 0.7 -0.606 4652 7082 4793 6851 0 -0.1806465
21137 0.4445191 1084 1104 223 55 59 26 100 100 1093 1080 216 70 71 17 100 100 1.006 1.039 0.008 1029 1023 1049 1010 0 0.4445191
8416 0.26200533 3071 3314 839 60 64 26 100 100 3239 3419 935 70 71 15 100 100 0.95 0.972 -0.074 3011 3169 3254 3349 0 0.26200533
10242 -1.8531581 712 681 275 64 68 26 94 91 6103 5629 1864 71 73 16 100 100 0.107 0.111 -3.219 648 6032 617 5558 0 -1.8531581
2905 0.051521048 351 375 135 57 61 27 100 100 601 654 240 72 74 17 99 99 0.556 0.546 -0.847 294 529 318 582 0 0.051521048
12687 -0.8563583 6129 6239 1905 62 66 26 100 100 17689 17668 4038 67 68 15 100 100 0.344 0.351 -1.538 6067 17622 6177 17601 0 -0.8563583
14466 0.1515051 75 79 33 58 62 25 35 13 160 187 113 70 72 16 99 99 0.189 0.179 -2.404 17 90 21 117 0 0.1515051
12682 0.22505517 1790 1674 641 62 66 26 96 96 2104 1970 789 74 75 16 94 91 0.851 0.85 -0.232 1728 2030 1612 1896 0 0.22505517
1164 0.10405272 4848 5516 3290 57 60 27 98 98 5564 6217 3417 69 70 17 99 98 0.872 0.888 -0.198 4791 5495 5459 6148 0 0.10405272
13497 0.20655382 334 344 113 62 67 26 100 100 503 525 125 71 74 16 100 100 0.63 0.621 -0.667 272 432 282 454 0 0.20655382
6298 -0.075196795 1023 1027 281 62 66 27 100 100 1647 1582 454 70 71 16 98 98 0.609 0.638 -0.715 961 1577 965 1512 0 -0.075196795
1338 -1.1285448 502 517 146 55 60 27 99 99 2229 2337 445 69 70 16 100 100 0.207 0.204 -2.273 447 2160 462 2268 0 -1.1285448
2074 -0.019658426 563 701 352 57 60 25 100 100 953 1123 488 71 71 16 100 100 0.574 0.612 -0.802 506 882 644 1052 0 -0.019658426
3639 0.56238836 5170 5475 1181 59 63 27 100 100 3843 3745 1118 73 74 16 100 99 1.356 1.475 0.439 5111 3770 5416 3672 0 0.56238836
17157 -0.44638205 212 225 101 56 61 26 98 95 577 593 141 74 74 16 100 100 0.31 0.326 -1.689 156 503 169 519 0 -0.44638205
16146 -1.0233257 595 603 149 58 61 24 100 100 2361 2387 339 69 70 16 100 100 0.234 0.235 -2.094 537 2292 545 2318 0 -1.0233257
21197 -0.41986063 218 238 82 55 59 27 99 96 573 575 103 67 65 21 100 100 0.322 0.36 -1.634 163 506 183 508 0 -0.41986063
21104 0.22628032 173 185 85 54 58 25 92 85 294 304 91 66 67 16 98 98 0.522 0.55 -0.938 119 228 131 238 0 0.22628032
16066 -1.4684769 91 91 38 57 61 25 54 30 488 496 102 70 72 15 100 100 0.081 0.08 -3.62 34 418 34 426 0 -1.4684769
20106 -0.34623995 2334 2543 839 56 61 28 100 100 4461 4736 955 69 71 16 100 100 0.519 0.533 -0.947 2278 4392 2487 4667 0 -0.34623995

Total number of rows: 21495

Table truncated, full table size 2573 Kbytes.




Supplementary data files not provided
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