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Sample GSM10330 Query DataSets for GSM10330
Status Public on Oct 29, 2003
Title Reciprocity-4h medium UV-B
Sample type RNA
 
Channel 1
Source name UV-B exposed
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name control
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 log 2 ratio UV-B/control
ratio (J-K)/(M-N) 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 (J-K)/(M-N) 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 -0.052095489 0.905574043 2370 193 271 2582 178 267 177 1253 0 1.104 1.149 0.5222 0.6611 0.7027 0.9944 1 0.9831 1 0.2139 0.1992 0 0.9221 0.00E+00 0.9697 0.00E+00
2 -0.058389515 0.901631913 2171 182 284 2370 164 300 177 1057 0 1.109 1.122 1.077 0.9165 1.192 1 0.9774 1 0.9661 0.1968 0.2188 0 0.9386 0.00E+00 0.8895 0.00E+00
3 -0.076089016 0.890637945 2331 181 381 2576 162 398 173 1013 0 1.123 1.106 1.051 0.8689 1.244 0.9942 0.9884 0.9884 0.9653 0.1843 0.2171 0 0.891 0.00E+00 0.8394 0.00E+00
4 -0.214860758 0.808959421 4217 190 500 5150 172 601 177 1013 0 1.236 1.162 1.1 0.9092 1.233 0.9435 0.9774 0.8814 0.9322 0.3555 0.3911 0 0.7067 0.00E+00 0.7497 0.00E+00
5 -0.036507906 0.915411356 3351 191 545 3629 177 624 177 1158 0 1.092 0.9971 0.9761 0.8726 1.137 0.8983 0.8362 0.8079 0.7853 0.3765 0.3998 0 0.6456 0.00E+00 0.625 0.00E+00
6 -0.373642261 0.724650744 3414 198 564 4626 188 593 177 1092 0 1.38 1.222 1.127 0.818 1.474 0.904 0.9379 0.8475 0.887 0.3928 0.4297 0 0.6678 0.00E+00 0.673 0.00E+00
7 -0.003787359 0.936410256 1126 213 563 1176 201 514 177 1038 0 1.068 0.9347 0.8494 0.7903 1.095 0.9887 0.9718 0.9096 0.9322 0.1985 0.2261 0 0.6395 0.00E+00 0.7066 0.00E+00
8 -0.030079924 0.919499106 724 210 515 757 198 453 177 1022 0 1.088 0.944 0.7296 0.6845 1.097 0.9661 0.9831 0.9492 0.9661 0.1468 0.1584 0 0.6492 0.00E+00 0.6951 0.00E+00
9 0.067744648 0.98400984 987 187 453 989 176 381 177 1001 0 1.016 0.9108 0.7401 0.7619 0.9627 0.9831 1 0.9661 0.9944 0.1933 0.2008 0 0.746 0.00E+00 0.7906 0.00E+00
10 2.136765014 4.128921569 8594 171 321 2200 160 286 177 1082 0 0.2422 0.2487 0.2328 0.9186 0.235 0.9266 0.8249 0.8249 0.7514 0.3802 0.3241 0 0.699 0.00E+00 0.6153 0.00E+00
11 2.203375837 4.324027916 8843 169 248 2162 156 221 177 1096 0 0.2313 0.2506 0.2144 0.9005 0.2166 0.9096 0.8927 0.7853 0.7627 0.3436 0.3049 0 0.6913 0.00E+00 0.6455 0.00E+00
12 2.060953317 3.917554423 8621 163 222 2308 149 178 177 1126 0 0.2553 0.258 0.2396 0.9096 0.2424 0.9153 0.8701 0.8023 0.7627 0.3361 0.3104 0 0.7388 0.00E+00 0.6802 0.00E+00
13 205 172 276 219 164 230 177 1052 0 1.667 1.674 0.09232 0.191 0.1188 0.6215 0.6723 0.1582 0.2994 0.1087 0.1573 1 0.1531 1.41E-03 0.2099 2.39E-06
14 0.227122293 1.098947368 1221 177 287 1126 176 258 177 1022 0 0.91 0.9466 0.562 0.7063 0.7254 0.8644 0.8079 0.6497 0.6497 0.2588 0.2873 0 0.5136 1.02E-35 0.516 4.64E-36
15 0.203335645 1.080976864 1003 162 202 935 157 190 177 1022 0 0.9251 0.9615 0.8542 0.882 0.9644 0.9492 0.8927 0.6836 0.7062 0.2979 0.3127 0 0.6305 0.00E+00 0.5614 1.34E-42
16 0.501220483 1.328888889 758 160 211 603 153 293 177 1022 0 0.7525 0.7945 0.1812 0.1858 0.8743 0.9492 0.9492 0.8192 0.8192 0.2268 0.2418 0 0.7194 0.00E+00 0.6862 0.00E+00
17 -0.226538169 0.802437999 2076 167 347 2539 160 364 177 1038 0 1.246 0.8102 0.8636 0.6411 1.577 0.9605 0.9492 0.8814 0.8588 0.3826 0.3895 0 0.7473 0.00E+00 0.7288 0.00E+00
18 392 168 372 288 160 336 177 1001 0 0.5714 0.6113 0.3186 0.4539 0.4821 0.9096 0.8701 0.7401 0.6384 0.1317 0.1546 0 0.573 3.22E-44 0.4774 7.79E-31
19 0.105993848 1.010447137 2582 164 219 2542 149 200 177 1090 0 0.9897 0.9566 0.9219 0.9206 1.001 0.9605 0.9379 0.8475 0.8644 0.3176 0.3106 0 0.7741 0.00E+00 0.7808 0.00E+00
20 0.123550572 1.022818792 2444 158 198 2379 144 175 177 1111 0 0.9777 0.9817 0.9102 0.9342 0.9725 0.9605 0.8927 0.774 0.8079 0.2727 0.2938 0 0.7205 0.00E+00 0.7358 0.00E+00

Total number of rows: 17296

Table truncated, full table size 2802 Kbytes.




Supplementary data files not provided
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