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Sample GSM132687 Query DataSets for GSM132687
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 12 hours compared with sorbitol control, replicate 1
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 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 0.023919465 1439 1480 361 59 66 34 100 100 1429 1488 311 80 82 31 100 100 1.023 1.009 0.033 1380 1349 1421 1408 0 0.023919465
21137 -0.25629494 504 512 144 48 52 23 100 100 715 752 187 83 86 32 100 100 0.722 0.694 -0.471 456 632 464 669 0 -0.25629494
8416 0.14613512 3726 4240 1273 54 60 24 100 100 3015 3322 815 74 78 28 100 100 1.249 1.289 0.32 3672 2941 4186 3248 0 0.14613512
10242 -0.09641225 1823 1853 391 59 63 25 100 100 1979 2026 370 84 87 29 100 100 0.931 0.924 -0.103 1764 1895 1794 1942 0 -0.09641225
2905 0.20363972 319 337 144 54 59 27 99 99 312 324 119 73 75 26 99 99 1.109 1.127 0.149 265 239 283 251 0 0.20363972
12687 -0.112265415 3511 3584 520 57 60 22 100 100 3630 3640 517 69 73 26 100 100 0.97 0.988 -0.044 3454 3561 3527 3571 0 -0.112265415
14466 -0.04522306 321 321 99 56 59 24 100 100 383 381 108 77 79 26 100 100 0.866 0.872 -0.208 265 306 265 304 0 -0.04522306
12682 0.004055372 2491 2535 451 58 64 25 100 100 2406 2454 397 91 93 33 100 100 1.051 1.048 0.072 2433 2315 2477 2363 0 0.004055372
1164 0.10504884 2252 2551 945 50 55 24 100 100 1986 2077 523 69 72 26 100 100 1.149 1.246 0.2 2202 1917 2501 2008 0 0.10504884
13497 -0.1536454 282 289 93 57 60 24 100 99 377 382 110 87 89 30 100 99 0.776 0.786 -0.366 225 290 232 295 0 -0.1536454
6298 0.13637355 576 593 209 54 58 25 98 98 568 582 163 76 78 26 100 100 1.061 1.065 0.085 522 492 539 506 0 0.13637355
1338 -0.05725412 645 662 193 50 53 22 100 100 733 729 170 67 70 26 100 100 0.893 0.924 -0.163 595 666 612 662 0 -0.05725412
2074 0.05403551 368 440 255 53 56 25 100 100 402 461 225 72 75 26 100 100 0.955 0.995 -0.067 315 330 387 389 0 0.05403551
3639 -0.29690102 8633 8689 1101 55 59 25 100 100 9561 9425 1081 82 85 29 100 100 0.905 0.924 -0.144 8578 9479 8634 9343 0 -0.29690102
17157 -0.35126764 228 242 94 55 60 26 98 95 359 366 110 87 90 33 100 98 0.636 0.67 -0.653 173 272 187 279 0 -0.35126764
16146 -0.1200434 412 432 126 53 58 23 100 100 519 514 137 75 79 28 100 100 0.809 0.863 -0.307 359 444 379 439 0 -0.1200434
21197 -0.43932047 218 242 114 52 63 41 95 89 368 401 168 83 96 228 65 20 0.582 0.597 -0.78 166 285 190 318 0 -0.43932047
21104 0.078192815 263 280 115 50 54 23 100 99 294 319 115 76 80 30 100 99 0.977 0.947 -0.033 213 218 230 243 0 0.078192815
16066 -0.21310703 153 158 76 55 59 24 89 76 230 252 100 86 90 31 96 87 0.681 0.62 -0.555 98 144 103 166 0 -0.21310703
20106 -0.089388244 367 388 140 49 54 24 100 100 466 485 170 82 86 31 100 100 0.828 0.841 -0.272 318 384 339 403 0 -0.089388244

Total number of rows: 21495

Table truncated, full table size 2581 Kbytes.




Supplementary data files not provided
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