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Sample GSM10328 Query DataSets for GSM10328
Status Public on Oct 29, 2003
Title reciprocity-2h high UV-B-2
Sample type RNA
 
Channel 1
Source name control
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name UV-B exposed
Organism Zea mays
Extracted molecule total RNA
 
 
Description Microarray hybridization was used to assess UV-B responses in both directly exposed and shielded tissues of a maize line deficient in anthocyanin accumulation. Among 347 transcripts found to be regulated after 8 h of high UV-B irradiation, 285 were increased significantly in at least one organ but only 80 were down-regulated by UV-B. Although some genes were regulated by UV-B in more than one sample, most UV-B regulated genes were organ-specific. A larger number of transcript changes occurred in directly exposed than in shielded organs, and more transcripts levels were changed in adult than in seedling tissues. Because shielded tissues including roots, immature ears, and leaves covered with a plastic that absorbs UV-B exhibited altered transcriptome profiles after plant exposure to UV-B, some signal(s) must be transmitted from irradiated to shielded tissues. The time course of transcript abundance changes monitored by RNA blot hybridization and real time RT-PCR indicated that the response kinetics to UV-B are very rapid as some transcript levels are altered within 1 h exposure, in both exposed and shielded tissues. As the same total UV-B irradiation dose applied at three intensities elicited different transcript profiles, transcriptome changes do not show reciprocity. Confirming and extending prior microarray hybridization results, supplemental UV-B increased expression of stress response and ribosomal protein genes, while photosynthesis-associated genes were down regulated in adult leaves.
 
Submission date Sep 18, 2003
Last update date May 28, 2005
Contact name Paula Casati
E-mail(s) casati@cefobi-conicet.gov.ar
Phone 54-341-4371955
Organization name Universidad Nacional de Rosario
Department Biological Sciences
Lab Casati
Street address Suipacha 531
City Rosario
State/province Santa Fe
ZIP/Postal code 2000
Country Argentina
 
Platform ID GPL499
Series (1)
GSE671 Rapid molecular responses of maize to UV-B: gene expression profiling in irradiated and shielded tissues

Data table header descriptions
ID_REF
VALUE log2 ratio UV-B/control
Ratio (M-N)/(J-K) UV-B/control
CH1I uncorrected mean pixel intensity for channel 1 (Cy3)
CH1B median background pixel intensity for channel 1 (Cy3)
CH1AB mean background pixel intensity for channel 1 (Cy3)
CH2I uncorrected mean pixel intensity for channel 2 (Cy5)
CH2B median background pixel intensity for channel 2 (Cy5)
CH2AB mean background pixel intensity for channel 2 (Cy5)
SPIX number of pixels in a spot
BGPIX uniform background in the two channels
EDGE
RAT2
MRAT median of (Ch2PI-CH2B)/(Ch1PI-CH1B)
REGR slope estimate by simple linear regression
CORR correlation between channel1 and channel 2 pixels within the spot
LFRAT slope estimate by least-squares fit
CH1GTB1 fraction of pixels in the spot greater than background (CH1B)
CH2GTB1 fraction of pixels in the spot greater than background (CH2B)
CH1GTB2 fraction of pixels in the spot greater than 1.5 times the background (CH1B)
CH2GTB2 fraction of pixels in the spot greater than 1.5 times the background (CH2B)
CH1EDGEA mean magnitude of the horizontal and vertical Sobel edge vectors contained within each spot (CH1)
CH2EDGEA mean magnitude of the horizontal and vertical Sobel edge vectors contained within each spot (CH2)
FLAG user defined spot flag
CH1KSD value of the Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity distribution is drawn from the background distribution
CH1KSP actual probability derived from CH1KSD
CH2KSD value of the Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity distribution is drawn from the background distribution
CH2KSP actual probability derived from CH2KSD

Data table
ID_REF VALUE Ratio (M-N)/(J-K) CH1I CH1B CH1AB CH2I CH2B CH2AB SPIX BGPIX EDGE RAT2 MRAT REGR CORR LFRAT CH1GTB1 CH2GTB1 CH1GTB2 CH2GTB2 CH1EDGEA CH2EDGEA FLAG CH1KSD CH1KSP CH2KSD CH2KSP
1 0.145941144 1.194114471 2001 149 212 2412.5 201 288.5416667 177 1305 0 1.194 1.173 1.084 0.9125 1.203 0.9605 0.9718 0.8644 0.9153 0.2223 0.227 0 0.8081 0.00E+00 0.8223 0.00E+00
2 0.08601573 1.145530388 1938 150 203 2255.208333 207 280.2083333 177 1154 0 1.146 1.152 1.102 0.9269 1.201 0.9661 0.9605 0.8475 0.887 0.2518 0.2614 0 0.7998 0.00E+00 0.7867 0.00E+00
3 0.027383678 1.099908626 2434 154 285 2719.791667 212 337.5 174 1115 0 1.1 1.101 1.014 0.9123 1.119 0.9885 0.9885 0.977 0.977 0.2327 0.2353 0 0.9002 0.00E+00 0.878 0.00E+00
4 0.064407232 1.128500636 3822 156 374 4352.083333 215 427.0833333 177 1049 0 1.129 0.9995 0.9967 0.8804 1.145 0.9492 0.9661 0.8983 0.9266 0.392 0.4057 0 0.7382 0.00E+00 0.7657 0.00E+00
5 -0.054228497 1.039414797 6033 149 447 6322.916667 207 486.4583333 177 1158 0 1.039 1.025 0.9106 0.8662 1.053 0.9887 0.9831 0.9209 0.9322 0.2774 0.282 0 0.8068 0.00E+00 0.8156 0.00E+00
6 0.173002298 1.216724297 3766 151 570 4611.458333 213 686.4583333 177 1092 0 1.217 1.065 1.061 0.8978 1.199 0.9435 0.9492 0.887 0.8983 0.405 0.4192 0 0.6636 0.00E+00 0.6788 0.00E+00
7 0.427333638 1.451287794 1048 155 605 1525 229 811.4583333 177 1038 0 1.451 1.313 1.045 0.8389 1.288 0.9605 0.9944 0.9322 0.9774 0.1798 0.1775 0 0.6502 0.00E+00 0.7071 0.00E+00
8 0.254193822 1.287162162 783 154 518 1040.625 231 715.625 177 1038 0 1.287 1.173 1.173 0.7963 1.602 0.9887 1 0.9831 0.9887 0.1573 0.1923 0 0.673 0.00E+00 0.6873 0.00E+00
9 0.355832252 1.381113851 956 145 429 1327.083333 207 578.125 177 1044 0 1.381 1.335 1.143 0.7812 1.602 1 0.9887 0.9718 0.9887 0.1598 0.1692 0 0.7756 0.00E+00 0.7933 0.00E+00
10 1.555362114 3.171932596 2036 137 257 6212.5 189 330.2083333 177 1118 0 3.172 3.014 2.742 0.9037 3.291 0.8644 0.9153 0.7571 0.8305 0.3085 0.365 0 0.6757 0.00E+00 0.7399 0.00E+00
11 1.532702567 3.122502153 2069 134 155 6226.041667 184 216.6666667 177 1090 0 3.123 3.089 2.973 0.9461 3.287 0.9153 0.8983 0.7175 0.8079 0.3466 0.3688 0 0.6875 0.00E+00 0.7436 0.00E+00
12 1.526937541 3.110049497 2188 134 144 6576.041667 188 195.8333333 177 1105 0 3.11 3.062 2.991 0.9504 3.279 0.9096 0.9322 0.7232 0.8249 0.3447 0.3611 0 0.729 0.00E+00 0.7683 0.00E+00
13 212 137 170 288.5416667 192 226.0416667 177 1037 0 1.287 1.474 0.8951 0.7299 1.302 0.7514 0.7627 0.3164 0.3559 0.1351 0.1629 1 0.3874 1.50E-20 0.2894 1.18E-11
14 0.284382103 1.314379699 935 137 197 1246.875 198 268.75 177 1022 0 1.314 1.364 1.276 0.9162 1.429 0.8475 0.8192 0.6215 0.6384 0.2657 0.2909 0 0.5307 4.09E-38 0.495 3.30E-33
15 0.325019189 1.351928815 919 137 301 1255.208333 198 461.4583333 177 1022 0 1.352 1.35 1.188 0.7123 1.977 0.8814 0.8249 0.5989 0.5819 0.2798 0.2844 0 0.5059 1.13E-34 0.4157 1.50E-23
16 415 140 365 470.8333333 198 580.2083333 177 1014 0 0.9921 1.146 0.978 0.5795 2.279 0.8079 0.8588 0.6667 0.661 0.1756 0.1845 0 0.5049 1.67E-34 0.4924 7.82E-33
17 328 142 387 402.0833333 208 685.4166667 177 1017 0 1.043 0.9343 1.18 0.5253 3.656 0.8418 0.8644 0.7232 0.6723 0.137 0.1556 0 0.5169 3.76E-36 0.4643 3.00E-29
18 272 138 271 345.8333333 204 450 177 968 0 1.058 1.02 2.161 0.8159 3.095 0.7288 0.7684 0.5593 0.5198 0.1195 0.1382 0 0.3956 3.42E-21 0.3611 9.78E-18
19 0.610638564 1.647911269 1676 132 184 2734.375 190 264.5833333 177 1057 0 1.648 1.689 1.563 0.9424 1.702 0.8814 0.8757 0.7458 0.7627 0.2602 0.2739 0 0.6835 0.00E+00 0.6853 0.00E+00
20 0.674684663 1.722715736 1511 132 169 2565.625 190 244.7916667 177 1075 0 1.723 1.814 1.65 0.9503 1.779 0.9322 0.887 0.8079 0.7797 0.3118 0.3022 0 0.7585 0.00E+00 0.7189 0.00E+00

Total number of rows: 17296

Table truncated, full table size 2980 Kbytes.




Supplementary data files not provided

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