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Sample GSM40315 Query DataSets for GSM40315
Status Public on Mar 02, 2005
Title NC_CBF3_1
Sample type RNA
 
Channel 1
Source name Ubi1::CBF3 transgenic rice leaves
Organism Oryza sativa
Extracted molecule total RNA
 
Channel 2
Source name Nontransgenic rice leaves
Organism Oryza sativa
Extracted molecule total RNA
 
 
Description Microarrays were hybridized with Cy3- and Cy5-labeled probe pairs of Ubi1::CBF3 and nontransgenic plants.
Transgenic and nontransgenic rice (Oryza sativa cv Nakdong) seeds were germinated on soil and grown in the greenhouse (16-h-light/8-h-dark cycles).
Total RNA (100 ¥ìg) was prepared from leaf tissues of 14-day-old transgenic and nontransgenic seedlings (5-10 plants each) and the mRNA was purified from total RNAs using Qiagen oligotex column (Qiagen, USA). Preparation of fluorescence labeled probes and microarray hybridization was performed as procedures provided by Genisphere 3DNA Array Detection Array 50 Kit (Version 2) (Genisphere, USA).
The microarray was scanned with Genepix 5.0B (Axon Instruments, USA) and the quality of chip data was analysed with statistical R language and sma package in Bioconductor (http://www.bioconductor.org/)implemented on Linux platform. Multivariate statistics was performed with Acuity 3.1 (Axon Instruments, USA).
Keywords = Abiotic stress, CBF3
 
Submission date Jan 31, 2005
Last update date Mar 20, 2006
Contact name Ju-Kon Kim
E-mail(s) jukon@bio.mju.ac.kr
Phone 82-31-330-6197
Fax 82-31-321-6355
Organization name Myongji University
Department Division of Bioscience and Bioinformatics
Lab Molecular Genetics
Street address 38-2 Nam-dong
City Yongin
State/province Kyonggi-do
ZIP/Postal code 449-728
Country South Korea
 
Platform ID GPL1829
Series (1)
GSE2211 Abiotic stress

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
SPOT_ADDR Spot address. 2 chips/1 set, 12 X 4 blocks/1 chip, 26 X 26 spots/1 block
CH1_Median CH1 (F635) median fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_Median
CH1_BKD_SD
CH2_Median CH2 (F532) median fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F532) background median fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
Flags Spot quality (50 and 0, good; -50 and -100, bad)
UNF_VALUE Log ratios with base 2 were adjusted by block-by-block Lowess normalizatio

Data table
ID_REF VALUE SPOT_ADDR CH1_Median CH1_SD CH1_BKD_Median CH1_BKD_SD CH2_Median CH2_SD CH2_BKD_Median CH2_BKD_SD Flags UNF_VALUE
Os000099_01 -0.38 A01010101 3256 1360 570 253 4329 2960 824 198 0 -0.38
Os000105_01 A01010102 663 298 539 248 826 252 824 190 -50 -0.012
Os000123_01 A01010103 701 336 548 254 864 285 826 187 -50 -0.027
Os000129_01 A01010104 543 258 584 294 777 260 834 219 -50 -0.207
Os000147_01 -0.595 A01010105 843 425 619 296 1379 507 890 286 0 -0.595
Os000153_01 -0.097 A01010106 6613 3408 588 268 7121 3445 844 347 0 -0.097
Os000171_01 0.077 A01010107 1028 440 577 259 1060 435 813 367 0 0.077
Os000177_01 A01010108 556 263 568 307 816 201 810 199 -50 -0.224
Os000473_01 -0.027 A01010109 856 339 594 350 977 303 824 285 0 -0.027
Os000479_01 A01010110 699 313 575 253 910 483 806 230 -50 -0.125
Os000497_01 -0.084 A01010111 1006 399 572 261 1155 346 817 189 0 -0.084
Os000502_01 0.107 A01010112 1265 547 567 248 1250 619 814 208 0 0.107
Os000520_01 0.178 A01010113 936 320 560 264 922 366 839 201 0 0.178
Os000526_01 0.087 A01010114 810 352 606 292 881 1284 808 254 0 0.087
Os000543_01 -0.094 A01010115 2074 687 580 272 2287 673 838 222 0 -0.094
Os000549_01 A01010116 901 387 606 467 993 366 842 496 -50 0.009
Os000842_01 0.248 A01010117 12932 6139 583 254 10835 4220 780 193 0 0.248
Os000848_01 A01010118 719 344 588 256 882 302 807 215 -50 -0.037
Os000865_01 -0.045 A01010119 816 309 590 250 955 265 802 232 0 -0.045
Os000871_01 A01010120 591 290 582 254 759 212 778 190 -50 -0.033

Total number of rows: 60727

Table truncated, full table size 4167 Kbytes.




Supplementary data files not provided
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