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Sample GSM10334 Query DataSets for GSM10334
Status Public on Oct 29, 2003
Title Reciprocity-8h high 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 0.991154824 2.253480278 4133 248 567 1909 185 323 177 1169 0 0.4438 0.4493 0.4165 0.7968 0.4546 0.9887 0.9266 0.9322 0.8757 0.2965 0.2821 0 0.8285 0.00E+00 0.7925 0.00E+00
2 1.020251971 2.299391256 4365 210 453 1970 163 283 177 1002 0 0.4349 0.4575 0.3739 0.8262 0.3964 0.9435 0.9435 0.9153 0.8644 0.259 0.2432 0 0.8315 0.00E+00 0.7839 0.00E+00
3 0.920737702 2.146130346 4394 179 428 2108 144 300 177 914 0 0.466 0.457 0.4681 0.8198 0.5123 0.9831 0.9435 0.9266 0.887 0.2437 0.2403 0 0.8491 0.00E+00 0.7844 0.00E+00
4 -0.183238472 0.998449612 4690 182 430 4661 146 372 177 891 0 1.002 1.071 0.8641 0.8784 0.9815 0.9492 0.9605 0.8983 0.9209 0.3962 0.4014 0 0.7804 0.00E+00 0.8029 0.00E+00
5 0.00785072 1.139855322 6799 181 455 5954 148 449 177 917 0 0.8773 0.9428 0.7849 0.8456 0.9157 0.9718 0.9379 0.9322 0.904 0.2879 0.295 0 0.8439 0.00E+00 0.7756 0.00E+00
6 -0.030392452 1.110036832 5009 187 568 4499 155 511 177 922 0 0.9009 0.8995 0.8159 0.8509 0.9519 0.9492 0.9322 0.8475 0.8531 0.3782 0.3716 0 0.644 0.00E+00 0.6544 0.00E+00
7 0.70487679 1.847887324 1508 196 634 879 169 469 177 955 0 0.5412 0.7603 0.1913 0.4672 0.2189 0.9944 1 0.9944 0.9944 0.233 0.2121 0 0.6875 0.00E+00 0.7139 0.00E+00
8 0.239525125 1.338414634 1085 207 543 829 173 368 177 942 0 0.7472 0.6987 0.4802 0.6797 0.6063 0.9887 0.9887 0.9661 0.9831 0.1857 0.186 0 0.6661 0.00E+00 0.7152 0.00E+00
9 0.23214544 1.331585845 1222 206 381 928 165 245 177 934 0 0.751 0.7796 0.5411 0.7858 0.626 1 1 0.9944 1 0.1696 0.1635 0 0.8402 0.00E+00 0.8768 0.00E+00
10 2.172750997 5.111515152 8631 197 266 1808 158 179 177 951 0 0.1956 0.2002 0.1847 0.9247 0.1857 0.887 0.8588 0.7853 0.7006 0.3617 0.3196 0 0.6661 0.00E+00 0.5931 0.00E+00
11 2.066927513 4.75 7927 194 253 1779 151 167 177 911 0 0.2105 0.229 0.1883 0.9037 0.1898 0.904 0.9153 0.8136 0.7853 0.335 0.3196 0 0.703 0.00E+00 0.6691 0.00E+00
12 2.104181865 4.87425546 7571 206 275 1675 164 182 177 969 0 0.2052 0.2091 0.186 0.9251 0.187 0.8305 0.8249 0.7062 0.6723 0.3251 0.3048 0 0.5962 0.00E+00 0.5823 1.40E-45
13 0.50053576 1.603846154 1446 195 304 946 166 207 177 985 0 0.6235 0.6189 0.5399 0.841 0.5941 1 0.9548 0.9548 0.8418 0.2541 0.2287 0 0.7665 0.00E+00 0.6887 0.00E+00
14 0.426050121 1.523141655 1261 175 254 868 155 197 177 940 0 0.6565 0.6222 0.6252 0.8915 0.673 1 0.9831 0.9661 0.8531 0.2672 0.243 0 0.8456 0.00E+00 0.7102 0.00E+00
15 0.356396817 1.451351351 1248 174 222 891 151 167 177 940 0 0.689 0.7098 0.6074 0.8681 0.6645 1 0.9774 0.9661 0.9209 0.2562 0.2684 0 0.8554 0.00E+00 0.803 0.00E+00
16 397 199 264 297 163 177 177 940 0 0.6768 0.6447 0.136 0.2345 0.1969 0.8814 0.8757 0.6893 0.6158 0.1647 0.1763 0 0.5389 8.40E-39 0.5108 6.71E-35
17 396 231 299 296 179 202 177 956 0 0.7091 0.7333 0.2039 0.458 0.2397 0.8079 0.8588 0.5593 0.5367 0.1498 0.1446 0 0.4504 2.71E-27 0.4376 8.58E-26
18 367 196 266 257 163 194 177 919 0 0.5497 0.5581 0.2858 0.5832 0.3341 0.7571 0.7571 0.6328 0.5028 0.1568 0.1478 1 0.4397 6.94E-26 0.3593 2.03E-17
19 0.124868244 1.236162362 1512 172 214 1228 144 166 177 941 0 0.809 0.8067 0.7535 0.9285 0.7988 0.8701 0.8644 0.7288 0.7232 0.2921 0.3155 0 0.6314 0.00E+00 0.6329 0.00E+00
20 0.141442333 1.250445633 1590 187 234 1279 157 178 177 956 0 0.7997 0.7892 0.7303 0.9019 0.7916 0.904 0.8927 0.7684 0.7684 0.3308 0.3145 0 0.6171 0.00E+00 0.6621 0.00E+00

Total number of rows: 17296

Table truncated, full table size 2859 Kbytes.




Supplementary data files not provided
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