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Sample GSM132685 Query DataSets for GSM132685
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 12 hours, 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 control treatment for 12 hours
Organism Oryza sativa
Characteristics As a control RNA, Oryza sativa cv Tainung67 suspension cells culture in medium within 3% sucrose for 12 hours.
Growth protocol Oryza sativa suspension cells cultured in Murashige and Skoog medium within 3% 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 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 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 -0.4666427 1390 1384 257 60 62 24 100 100 1841 1813 267 47 47 8 100 100 0.741 0.75 -0.432 1330 1794 1324 1766 0 -0.4666427
21137 0.05676749 839 864 157 53 58 23 100 100 702 720 89 42 43 8 100 100 1.191 1.196 0.252 786 660 811 678 0 0.05676749
8416 0.3245778 880 852 261 61 65 25 98 97 649 613 177 45 45 7 97 97 1.356 1.393 0.439 819 604 791 568 0 0.3245778
10242 -0.7029448 200 207 71 63 66 25 99 93 528 516 103 47 47 7 100 100 0.285 0.307 -1.812 137 481 144 469 0 -0.7029448
2905 -0.09967305 170 175 67 55 59 24 95 86 186 187 39 43 44 6 100 100 0.804 0.833 -0.314 115 143 120 144 0 -0.09967305
12687 0.5172742 4308 4094 1150 62 65 23 100 100 3074 2985 783 45 46 7 100 99 1.402 1.371 0.487 4246 3029 4032 2940 0 0.5172742
14466 0.09807074 86 87 30 61 66 26 46 21 59 59 19 47 47 9 57 30 2.083 2.167 1.059 25 12 26 12 0 0.09807074
12682 -0.59868026 1181 1172 255 62 66 24 100 100 846 828 135 46 46 7 100 100 1.399 1.419 0.484 1119 800 1110 782 0 -0.59868026
1164 0.20741777 4329 4221 979 53 58 25 100 100 3087 3107 711 42 43 10 100 100 1.404 1.36 0.49 4276 3045 4168 3065 0 0.20741777
13497 0.033458333 167 172 65 61 64 23 92 80 172 168 43 46 46 7 99 97 0.841 0.91 -0.249 106 126 111 122 0 0.033458333
6298 -0.51196647 677 667 213 58 62 25 99 99 701 682 138 46 46 7 100 100 0.945 0.958 -0.082 619 655 609 636 0 -0.51196647
1338 -0.24600488 621 637 173 55 59 24 100 99 852 855 188 42 42 6 100 100 0.699 0.716 -0.517 566 810 582 813 0 -0.24600488
2074 0.15469399 161 165 67 56 60 23 87 82 191 186 44 43 44 7 98 98 0.709 0.762 -0.495 105 148 109 143 0 0.15469399
3639 0.33038718 4894 4607 1334 59 62 25 100 100 3612 3317 905 44 44 7 100 100 1.355 1.39 0.438 4835 3568 4548 3273 0 0.33038718
17157 0.16680658 138 145 62 59 62 25 80 65 156 153 31 45 45 7 99 99 0.712 0.796 -0.491 79 111 86 108 0 0.16680658
16146 -0.2782705 576 560 167 59 61 24 99 98 649 620 154 45 46 7 98 98 0.856 0.871 -0.224 517 604 501 575 0 -0.2782705
21197 -0.37228677 170 168 56 54 57 22 96 92 174 174 31 43 44 7 100 100 0.885 0.87 -0.175 116 131 114 131 0 -0.37228677
21104 0.19641635 91 97 40 55 58 24 62 37 83 82 14 42 43 10 95 90 0.878 1.05 -0.188 36 41 42 40 0 0.19641635
16066 -0.20949642 95 95 42 61 64 24 54 29 122 123 26 45 46 7 99 98 0.442 0.436 -1.179 34 77 34 78 0 -0.20949642
20106 0.13578726 600 579 168 55 59 25 99 98 518 493 108 43 43 7 100 100 1.147 1.164 0.198 545 475 524 450 0 0.13578726

Total number of rows: 21495

Table truncated, full table size 2433 Kbytes.




Supplementary data files not provided
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