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Sample GSM132688 Query DataSets for GSM132688
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 12 hours compared with sorbitol control, replicate 2
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 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 -0.00938027 1679 1752 451 63 269 2483 2 0 2150 2195 366 91 263 2638 8 0 0.785 0.803 -0.35 1616 2059 1689 2104 0 -0.00938027
21137 -0.2005224 451 458 125 53 58 26 100 100 796 806 167 90 93 32 100 100 0.564 0.566 -0.827 398 706 405 716 0 -0.2005224
8416 -0.018653985 3422 3468 986 60 64 25 100 100 4116 4090 686 84 87 30 100 100 0.834 0.851 -0.262 3362 4032 3408 4006 0 -0.018653985
10242 -0.16319224 1790 1786 279 61 65 25 100 100 2626 2603 326 92 96 33 100 100 0.682 0.687 -0.551 1729 2534 1725 2511 0 -0.16319224
2905 0.33991924 203 209 78 55 61 32 96 89 278 288 90 85 92 128 77 29 0.767 0.759 -0.383 148 193 154 203 0 0.33991924
12687 -1.14E-04 4090 4181 687 59 63 24 100 100 4748 4805 849 81 83 29 100 100 0.864 0.873 -0.211 4031 4667 4122 4724 0 -1.14E-04
14466 0.04058744 276 282 88 57 62 24 100 100 435 435 107 91 94 33 100 100 0.637 0.654 -0.651 219 344 225 344 0 0.04058744
12682 0.12387685 2498 2472 402 61 65 25 100 100 2732 2742 423 100 101 31 100 100 0.926 0.913 -0.111 2437 2632 2411 2642 0 0.12387685
1164 0.10432845 3220 3484 988 54 60 27 100 100 3482 3551 663 83 86 33 100 100 0.931 0.989 -0.102 3166 3399 3430 3468 0 0.10432845
13497 -0.09920028 197 198 73 60 64 25 93 89 368 372 96 99 102 36 100 98 0.509 0.505 -0.973 137 269 138 273 0 -0.09920028
6298 0.062402483 589 609 190 57 61 24 100 100 797 810 174 87 91 30 100 100 0.749 0.763 -0.416 532 710 552 723 0 0.062402483
1338 0.16622515 908 936 282 54 58 25 100 100 1051 1061 216 77 80 28 100 100 0.877 0.896 -0.19 854 974 882 984 0 0.16622515
2074 0.024482876 343 347 118 56 61 26 100 99 521 548 226 84 87 31 99 99 0.657 0.627 -0.607 287 437 291 464 0 0.024482876
3639 -0.28567272 8437 8301 1266 57 61 25 100 100 11889 11544 2399 90 93 31 100 100 0.71 0.72 -0.494 8380 11799 8244 11454 0 -0.28567272
17157 -0.3538075 151 158 62 58 62 25 90 76 350 352 120 101 105 36 98 95 0.373 0.398 -1.421 93 249 100 251 0 -0.3538075
16146 0.010219038 453 465 136 55 60 24 100 100 668 656 139 87 91 32 100 100 0.685 0.721 -0.546 398 581 410 569 0 0.010219038
21197 -0.40373003 141 151 62 55 63 34 84 61 336 345 101 91 92 38 100 100 0.351 0.378 -1.51 86 245 96 254 0 -0.40373003
21104 0.008598448 153 162 59 51 56 24 97 85 281 288 91 87 91 33 99 95 0.526 0.552 -0.927 102 194 111 201 0 0.008598448
16066 -0.023350567 107 112 48 58 63 25 66 48 214 226 70 97 100 35 95 81 0.419 0.419 -1.256 49 117 54 129 0 -0.023350567
20106 -0.020418383 288 308 123 53 57 24 99 99 479 501 158 93 97 35 100 100 0.609 0.625 -0.716 235 386 255 408 0 -0.020418383

Total number of rows: 21495

Table truncated, full table size 2566 Kbytes.




Supplementary data files not provided
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