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Sample GSM132690 Query DataSets for GSM132690
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 12 hours compared with sorbitol control, 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 sorbitol treatment for 12 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in suc free medium within sorbitol for 12 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose but with 88mM sorbitol 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 Suc-starved cells treated with sorbitol 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 sorbitol control 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 -0.12484697 1440 1387 565 78 434 3904 0 0 2174 2178 375 78 436 4152 0 0 0.65 0.623 -0.622 1362 2096 1309 2100 0 -0.12484697
21137 -0.20990853 365 366 151 63 72 42 95 92 684 705 166 73 79 35 100 100 0.494 0.479 -1.017 302 611 303 632 0 -0.20990853
8416 -0.012026516 2921 3057 1163 72 78 38 100 98 3711 4134 1213 78 81 31 100 100 0.784 0.736 -0.351 2849 3633 2985 4056 0 -0.012026516
10242 -0.062083855 2178 2160 504 75 87 121 100 100 2985 2930 654 79 177 1633 96 27 0.724 0.731 -0.467 2103 2906 2085 2851 0 -0.062083855
2905 0.1387117 211 231 97 65 73 39 95 84 327 348 112 71 77 33 100 99 0.57 0.599 -0.81 146 256 166 277 0 0.1387117
12687 -0.28846493 5825 5671 1584 73 79 40 99 98 9021 9191 1368 75 79 32 100 100 0.643 0.614 -0.637 5752 8946 5598 9116 0 -0.28846493
14466 0.051021498 280 291 104 68 74 38 97 92 442 442 139 77 83 35 98 98 0.581 0.611 -0.784 212 365 223 365 0 0.051021498
12682 0.10505421 2264 2244 718 76 81 37 99 99 2649 2718 688 78 83 33 100 100 0.851 0.821 -0.233 2188 2571 2168 2640 0 0.10505421
1164 0.17747554 5199 5282 2328 64 73 40 99 98 5247 5237 2503 69 75 33 95 93 0.992 1.01 -0.012 5135 5178 5218 5168 0 0.17747554
13497 -0.13775362 228 228 94 73 77 35 88 83 418 433 124 78 82 37 100 100 0.456 0.437 -1.133 155 340 155 355 0 -0.13775362
6298 -0.025633646 597 608 188 73 79 39 100 100 895 885 239 75 79 31 100 100 0.639 0.66 -0.646 524 820 535 810 0 -0.025633646
1338 0.047339708 698 698 204 60 68 37 100 100 976 960 306 68 72 31 97 95 0.703 0.715 -0.509 638 908 638 892 0 0.047339708
2074 0.25119796 340 365 172 67 75 39 96 91 446 485 172 74 79 33 100 100 0.734 0.725 -0.446 273 372 298 411 0 0.25119796
3639 -0.3013391 6749 6581 1144 72 79 40 100 100 10442 10068 1743 76 80 33 100 100 0.644 0.651 -0.635 6677 10366 6509 9992 0 -0.3013391
17157 -0.36401233 158 169 81 73 80 48 71 44 345 373 132 76 83 35 100 98 0.316 0.323 -1.662 85 269 96 297 0 -0.36401233
16146 0.04800962 338 346 171 63 70 36 91 85 526 514 224 77 81 32 90 89 0.612 0.648 -0.707 275 449 283 437 0 0.04800962
21197 -0.62178504 125 133 64 66 73 43 63 31 333 343 104 69 71 34 100 100 0.223 0.245 -2.162 59 264 67 274 0 -0.62178504
21104 0.1108691 122 129 64 63 71 41 62 35 218 222 79 72 75 31 94 87 0.404 0.44 -1.307 59 146 66 150 0 0.1108691
16066 -0.4166392 97 106 54 70 76 37 42 22 215 216 75 77 81 34 94 84 0.196 0.259 -2.354 27 138 36 139 0 -0.4166392
20106 0.00501126 257 275 137 63 69 35 94 88 429 447 180 74 78 32 99 99 0.546 0.568 -0.872 194 355 212 373 0 0.00501126

Total number of rows: 21495

Table truncated, full table size 2537 Kbytes.




Supplementary data files not provided

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