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Sample GSM132686 Query DataSets for GSM132686
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 12 hours, replicate 3
Sample type RNA
 
Channel 1
Source name Oryza sativa suspension cells under suc starvation for 12 hours
Organism Oryza sativa
Characteristics Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 12 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose for 12 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 12 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 12 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% sucrose for 12 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 12 hours, replecate 3
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 -0.001610025 757 761 201 92 104 62 100 100 937 969 188 120 122 40 100 100 0.814 0.788 -0.297 665 817 669 849 0 -0.001610025
21137 -0.20652726 556 578 187 80 89 51 99 98 938 928 178 119 122 43 100 100 0.581 0.616 -0.783 476 819 498 809 0 -0.20652726
8416 -0.56196856 2619 2674 492 92 99 51 100 100 3966 4020 539 116 121 42 100 100 0.656 0.661 -0.607 2527 3850 2582 3904 0 -0.56196856
10242 -0.031800445 1337 1339 253 94 99 48 100 100 1321 1299 229 116 119 40 100 100 1.032 1.052 0.045 1243 1205 1245 1183 0 -0.031800445
2905 0.19253163 175 181 90 85 93 50 65 45 539 543 105 118 122 42 100 100 0.214 0.226 -2.226 90 421 96 425 0 0.19253163
12687 0.1989526 2864 2865 484 93 102 52 100 100 2128 2125 255 158 161 50 100 100 1.407 1.409 0.492 2771 1970 2772 1967 0 0.1989526
14466 -0.39754796 484 482 175 88 96 48 98 97 987 989 212 116 118 40 100 99 0.455 0.451 -1.137 396 871 394 873 0 -0.39754796
12682 0.5673484 1621 1629 308 93 101 51 100 100 958 961 178 119 123 42 100 100 1.821 1.824 0.865 1528 839 1536 842 0 0.5673484
1164 0.21299598 2996 2942 558 81 90 51 100 100 2159 2267 484 123 126 45 100 100 1.432 1.334 0.518 2915 2036 2861 2144 0 0.21299598
13497 0.7063178 167 179 85 89 97 49 65 38 423 433 98 123 125 41 100 100 0.26 0.29 -1.943 78 300 90 310 0 0.7063178
6298 0.05599015 429 432 143 88 98 54 100 95 730 715 169 118 122 42 99 99 0.557 0.576 -0.844 341 612 344 597 0 0.05599015
1338 -0.6625983 774 799 233 91 101 56 100 100 1494 1507 286 130 140 100 100 100 0.501 0.514 -0.998 683 1364 708 1377 0 -0.6625983
2074 0.057876397 186 207 97 81 91 53 80 49 594 599 138 118 122 39 100 99 0.221 0.262 -2.181 105 476 126 481 0 0.057876397
3639 0.8698006 5259 5241 693 82 91 48 100 100 2003 2014 289 119 122 44 100 100 2.748 2.722 1.458 5177 1884 5159 1895 0 0.8698006
17157 0.20518348 121 137 72 88 97 50 43 22 451 446 98 119 122 41 99 99 0.099 0.15 -3.331 33 332 49 327 0 0.20518348
16146 -0.17666726 1302 1310 284 88 114 440 100 88 1472 1464 267 118 153 749 97 30 0.897 0.908 -0.157 1214 1354 1222 1346 0 -0.17666726
21197 0.084496886 150 156 70 84 91 50 58 32 531 542 109 112 113 47 100 100 0.158 0.167 -2.666 66 419 72 430 0 0.084496886
21104 -0.011582315 150 155 73 79 88 54 59 31 570 580 113 119 122 41 100 100 0.157 0.165 -2.667 71 451 76 461 0 -0.011582315
16066 -0.07263183 103 114 55 87 96 51 32 11 463 466 107 114 117 38 100 100 0.046 0.077 -4.447 16 349 27 352 0 -0.07263183
20106 0.5756259 219 222 111 81 90 50 77 62 481 486 116 111 117 43 100 99 0.373 0.376 -1.423 138 370 141 375 0 0.5756259

Total number of rows: 21495

Table truncated, full table size 2582 Kbytes.




Supplementary data files not provided
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