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Sample GSM132692 Query DataSets for GSM132692
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 24 hours, replicate 3
Sample type RNA
 
Channel 1
Source name Oryza sativa suspension cells under suc starvation for 24 hours
Organism Oryza sativa
Characteristics Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 24 hours
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose for 24 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 24 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 24 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% sucrose for 24 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 24 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 -0.38624027 1198 1196 291 111 124 69 100 100 2251 2247 429 148 152 57 100 100 0.517 0.517 -0.952 1087 2103 1085 2099 0 -0.38624027
21137 -0.061458956 604 608 205 99 110 62 98 96 1006 964 330 139 146 63 93 91 0.582 0.617 -0.78 505 867 509 825 0 -0.061458956
8416 -0.6869397 1315 1276 454 101 117 65 97 95 3311 3219 790 132 138 55 99 99 0.382 0.381 -1.389 1214 3179 1175 3087 0 -0.6869397
10242 -0.6055702 821 782 290 113 123 65 94 92 1913 1908 355 142 148 58 99 99 0.4 0.379 -1.323 708 1771 669 1766 0 -0.6055702
2905 -0.053583175 311 316 137 109 120 65 83 68 651 624 178 136 144 60 97 97 0.392 0.424 -1.35 202 515 207 488 0 -0.053583175
12687 -0.15828766 1899 1789 628 110 118 61 96 95 2921 2884 584 125 131 52 100 100 0.64 0.609 -0.644 1789 2796 1679 2759 0 -0.15828766
14466 -0.8051747 633 663 237 112 121 63 97 97 1811 1736 518 141 145 57 97 97 0.312 0.345 -1.68 521 1670 551 1595 0 -0.8051747
12682 0.42664415 1487 1487 315 113 124 63 100 100 1337 1328 337 141 144 55 99 99 1.149 1.158 0.2 1374 1196 1374 1187 0 0.42664415
1164 0.19232757 1921 1899 598 109 116 60 100 96 2104 2140 547 134 142 132 99 99 0.92 0.892 -0.121 1812 1970 1790 2006 0 0.19232757
13497 0.35158524 412 401 176 116 126 62 89 79 602 594 151 141 145 52 100 98 0.642 0.629 -0.639 296 461 285 453 0 0.35158524
6298 0.022798916 702 654 253 110 120 64 94 90 1032 1015 250 133 135 54 99 99 0.659 0.617 -0.603 592 899 544 882 0 0.022798916
1338 -0.8778537 655 679 261 103 115 60 95 95 1988 1956 521 129 139 104 99 99 0.297 0.315 -1.752 552 1859 576 1827 0 -0.8778537
2074 -0.06734002 306 337 123 107 118 63 95 80 653 667 169 136 144 58 99 97 0.385 0.433 -1.377 199 517 230 531 0 -0.06734002
3639 0.5644045 4335 4044 1233 111 120 62 99 98 3505 3534 575 137 143 55 100 100 1.254 1.158 0.327 4224 3368 3933 3397 0 0.5644045
17157 0.47335777 302 316 132 111 121 61 89 70 498 494 132 139 146 56 100 97 0.532 0.577 -0.91 191 359 205 355 0 0.47335777
16146 -0.42795336 1197 1226 372 112 120 61 99 98 2329 2146 668 133 139 58 96 96 0.494 0.553 -1.017 1085 2196 1114 2013 0 -0.42795336
21197 0.049173787 302 313 144 104 114 60 85 75 613 604 182 135 140 60 95 95 0.414 0.446 -1.272 198 478 209 469 0 0.049173787
21104 0.042679895 213 230 112 103 109 57 72 48 546 546 127 135 139 56 100 98 0.268 0.309 -1.902 110 411 127 411 0 0.042679895
16066 0.23087138 239 263 107 113 120 59 80 53 516 529 155 138 142 54 98 95 0.333 0.384 -1.585 126 378 150 391 0 0.23087138
20106 0.20857829 437 451 177 104 117 68 95 86 690 708 227 137 144 60 95 95 0.602 0.608 -0.732 333 553 347 571 0 0.20857829

Total number of rows: 21495

Table truncated, full table size 2632 Kbytes.




Supplementary data files not provided
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