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Sample GSM132694 Query DataSets for GSM132694
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 48 hours, replicate 2
Sample type RNA
 
Channel 1
Source name Oryza sativa suspension cells under suc starvation for 48 hours
Organism Oryza sativa
Characteristics Oryza sativa cv Tainung67 suspension cells culture in suc free medium for 48 hours
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium without sucrose for 48 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 48 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 48 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% sucrose for 48 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 48 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 -0.3206559 850 866 204 67 70 33 100 100 1334 1327 146 46 46 10 100 100 0.608 0.624 -0.718 783 1288 799 1281 0 -0.3206559
21137 -0.6477929 268 271 114 60 66 33 95 90 555 532 129 41 41 6 100 100 0.405 0.43 -1.305 208 514 211 491 0 -0.6477929
8416 0.008282007 752 737 261 67 71 30 97 96 865 825 220 43 44 8 99 98 0.833 0.857 -0.263 685 822 670 782 0 0.008282007
10242 -1.651034 170 175 77 68 74 35 80 65 747 744 111 46 46 7 100 100 0.146 0.153 -2.781 102 701 107 698 0 -1.651034
2905 -0.45156926 96 103 52 63 68 32 50 27 117 116 24 42 42 6 98 98 0.44 0.541 -1.184 33 75 40 74 0 -0.45156926
12687 -1.4360667 993 1001 192 67 75 36 100 100 4726 4794 427 44 44 7 100 100 0.198 0.197 -2.338 926 4682 934 4750 0 -1.4360667
14466 75 78 35 66 72 33 25 6 63 63 11 44 44 7 86 62 0.474 0.632 -1.078 9 19 12 19 -50
12682 -0.3446665 369 373 128 74 77 32 98 97 572 565 103 46 46 7 99 99 0.561 0.576 -0.834 295 526 299 519 0 -0.3446665
1164 -0.35042074 1726 1740 281 60 65 33 100 100 2948 2969 271 41 41 7 100 100 0.573 0.574 -0.803 1666 2907 1680 2928 0 -0.35042074
13497 -0.039318193 124 135 70 66 71 31 67 47 128 129 20 45 45 6 100 100 0.699 0.821 -0.517 58 83 69 84 0 -0.039318193
6298 0.10677191 596 572 220 67 74 34 96 94 625 586 161 44 44 7 98 97 0.91 0.932 -0.135 529 581 505 542 0 0.10677191
1338 -0.6895116 411 418 167 58 63 30 96 96 900 864 216 40 40 6 98 98 0.41 0.437 -1.285 353 860 360 824 0 -0.6895116
2074 0.10304066 181 200 92 60 67 32 90 81 187 187 27 42 42 7 100 100 0.834 0.966 -0.261 121 145 140 145 0 0.10304066
3639 0.24546443 3714 3561 791 64 71 34 100 100 3706 3554 739 43 43 6 100 100 0.996 0.996 -0.005 3650 3663 3497 3511 0 0.24546443
17157 -0.86714095 87 95 47 65 69 32 40 21 121 121 20 44 45 7 100 99 0.286 0.39 -1.807 22 77 30 77 0 -0.86714095
16146 1.2158222 643 623 222 64 71 32 96 95 263 242 76 43 43 6 97 95 2.632 2.809 1.396 579 220 559 199 0 1.2158222
21197 -1.055655 99 111 51 59 66 34 56 30 197 184 55 41 41 6 97 93 0.256 0.364 -1.963 40 156 52 143 0 -1.055655
21104 0.4243854 112 119 58 60 65 32 63 43 90 90 17 41 41 8 100 100 1.061 1.204 0.086 52 49 59 49 0 0.4243854
16066 -0.648513 81 86 35 65 71 34 36 9 91 89 14 45 47 11 98 90 0.348 0.477 -1.524 16 46 21 44 0 -0.648513
20106 -0.17375287 270 275 103 63 68 32 95 93 364 347 91 41 41 6 99 99 0.641 0.693 -0.642 207 323 212 306 0 -0.17375287

Total number of rows: 21495

Table truncated, full table size 2369 Kbytes.




Supplementary data files not provided
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