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Sample GSM130785 Query DataSets for GSM130785
Status Public on Sep 20, 2006
Title Rice suspension cells under suc starvation for 12 hours, 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 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 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 25, 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 -0.4823665 2317 2362 536 64 72 40 100 100 3887 3812 781 62 61 15 100 100 0.589 0.613 -0.764 2253 3825 2298 3750 0 -0.4823665
21137 -0.038656246 491 500 141 54 59 28 100 100 521 520 84 56 58 12 100 100 0.94 0.961 -0.09 437 465 446 464 0 -0.038656246
8416 0.09076201 2281 2376 575 61 65 26 100 100 1793 2030 759 60 61 12 100 100 1.281 1.175 0.357 2220 1733 2315 1970 0 0.09076201
10242 -1.380585 1907 1908 346 62 68 28 100 100 4040 4021 546 61 62 12 100 100 0.464 0.466 -1.109 1845 3979 1846 3960 0 -1.380585
2905 -0.25467858 379 383 110 59 63 28 98 98 468 475 146 58 58 14 100 100 0.78 0.777 -0.358 320 410 324 417 0 -0.25467858
12687 0.25314513 6910 6589 1923 64 67 25 100 100 4296 4496 1377 57 57 11 100 100 1.615 1.47 0.692 6846 4239 6525 4439 0 0.25314513
14466 0.91629076 96 108 55 60 63 26 54 32 120 122 32 60 60 12 95 88 0.6 0.774 -0.737 36 60 48 62 0 0.91629076
12682 0.124015756 1836 1834 293 64 68 28 100 100 3515 3627 714 60 60 11 100 100 0.513 0.496 -0.963 1772 3455 1770 3567 0 0.124015756
1164 0.25569844 4914 5078 976 57 61 27 100 100 4197 4616 1487 58 62 75 100 100 1.173 1.102 0.231 4857 4139 5021 4558 0 0.25569844
13497 -0.190181 292 303 116 62 65 26 99 98 331 358 128 61 62 12 100 100 0.852 0.811 -0.231 230 270 241 297 0 -0.190181
6298 -0.26534647 851 864 217 58 62 26 100 100 1525 1525 270 60 60 11 100 100 0.541 0.55 -0.886 793 1465 806 1465 0 -0.26534647
1338 -0.5691549 939 934 250 54 59 26 100 100 1309 1384 401 55 58 58 100 100 0.706 0.662 -0.503 885 1254 880 1329 0 -0.5691549
2074 -0.37509868 356 443 265 57 61 26 100 100 362 488 350 58 59 13 100 100 0.984 0.898 -0.024 299 304 386 430 0 -0.37509868
3639 0.23172905 6580 6476 857 58 63 27 100 100 4919 4929 859 60 61 12 100 100 1.342 1.318 0.425 6522 4859 6418 4869 0 0.23172905
17157 -0.32112142 217 230 105 59 62 26 94 89 232 253 98 62 63 12 100 98 0.929 0.895 -0.106 158 170 171 191 0 -0.32112142
16146 -0.3622544 2183 2142 488 58 61 25 100 100 3063 3101 584 58 58 13 100 100 0.707 0.685 -0.5 2125 3005 2084 3043 0 -0.3622544
21197 -0.15121329 129 133 60 56 102 1007 0 0 203 207 50 56 90 888 0 0 0.497 0.51 -1.01 73 147 77 151 0 -0.15121329
21104 0.088589735 244 284 159 55 59 27 99 93 249 273 106 55 57 12 100 100 0.974 1.05 -0.038 189 194 229 218 0 0.088589735
16066 -0.6764704 81 85 43 61 63 26 44 23 116 124 67 62 62 12 98 84 0.37 0.387 -1.433 20 54 24 62 0 -0.6764704
20106 -0.05575811 1851 1830 603 56 61 26 99 99 1761 1863 621 59 60 12 100 100 1.055 0.983 0.077 1795 1702 1774 1804 0 -0.05575811

Total number of rows: 21495

Table truncated, full table size 2532 Kbytes.




Supplementary data files not provided
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