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Sample GSM10315 Query DataSets for GSM10315
Status Public on Oct 29, 2003
Title roots-8h UV-B
Sample type RNA
 
Channel 1
Source name UV-B exposed plants
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name control plants
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 GPL498
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 1220 724 920 674 307 371 156 949 0 0.7399 0.7143 0.1172 0.3582 0.129 0.9551 0.9423 0.7756 0.859 0.08233 0.1087 0 0.7124 0.00E+00 0.707 0.00E+00
2 1095 723 861 600 315 391 156 763 0 0.7661 0.7878 0.4958 0.7107 0.6083 0.8205 0.8654 0.6154 0.7372 0.08939 0.1358 0 0.4802 5.89E-27 0.5585 2.54E-36
3 1118 693 822 672 307 378 156 763 0 0.8588 0.9661 0.5068 0.6888 0.6452 0.8782 0.9103 0.6603 0.7756 0.09544 0.131 0 0.5973 1.79E-41 0.6446 0.00E+00
4 1411 713 937 819 316 478 156 763 0 0.7206 1.25 0.1134 0.3959 0.1217 0.8333 0.7628 0.5064 0.609 0.1435 0.1661 0 0.3911 4.97E-18 0.4124 5.39E-20
5 976 741 954 713 329 479 156 763 0 1.634 1.553 0.6222 0.6492 0.9366 0.7115 0.7244 0.3718 0.5385 0.07256 0.1609 0 0.2717 6.40E-09 0.3649 9.49E-16
6 1019 716 840 776 308 379 156 763 0 1.545 1.405 0.8152 0.7263 1.172 0.7436 0.7885 0.4872 0.6346 0.08739 0.1694 0 0.3445 4.39E-14 0.461 7.01E-25
7 1136 711 813 865 306 371 156 763 0 1.315 1.235 1.029 0.8511 1.25 0.8077 0.859 0.5 0.6795 0.106 0.1699 0 0.4194 1.14E-20 0.5214 1.05E-31
8 1168 735 835 876 312 375 156 763 0 1.303 1.245 0.9728 0.8311 1.208 0.7179 0.7564 0.5 0.5962 0.09178 0.1617 0 0.3726 2.12E-16 0.4667 1.73E-25
9 1211 772 995 907 328 597 156 763 0 1.319 1.266 1.197 0.851 1.488 0.75 0.7372 0.4936 0.5962 0.1075 0.1763 0 0.3693 4.06E-16 0.4382 1.60E-22
10 1947 785 1173 2672 341 884 156 763 0 2.006 2.003 1.601 0.8703 1.991 0.8269 0.8974 0.7051 0.7885 0.1376 0.2165 0 0.451 7.82E-24 0.5642 4.70E-37
11 1754 751 1059 2369 326 698 156 763 0 2.037 1.963 1.501 0.8566 1.904 0.7885 0.7949 0.6282 0.6923 0.1277 0.2071 0 0.4291 1.29E-21 0.5474 6.59E-35
12 -0.608776502 0.655752587 2521 717 988 3503 312 531 156 718 0 1.769 1.791 1.192 0.7666 1.758 1 1 0.9872 1 0.1218 0.1785 0 0.8847 0.00E+00 0.9198 0.00E+00
13 -0.286625922 0.819817152 19994 720 982 27582 312 512 156 689 0 1.415 1.451 1.333 0.9425 1.443 0.9808 0.9936 0.9615 0.9936 0.2748 0.2996 0 0.8858 0.00E+00 0.9404 0.00E+00
14 -0.328851606 0.796169988 18942 736 1216 26843 319 828 156 776 0 1.457 1.458 1.369 0.9474 1.473 0.9744 1 0.9423 0.9936 0.2926 0.3156 0 0.8536 0.00E+00 0.9101 0.00E+00
15 -0.279865613 0.823667738 19712 743 1074 27026 313 834 156 756 0 1.408 1.454 1.351 0.9464 1.455 0.9359 0.9231 0.9038 0.8718 0.2872 0.3138 0 0.85 0.00E+00 0.814 0.00E+00
16 -0.548406434 0.683774993 5934 747 800 9110 311 514 156 725 0 1.696 1.694 1.604 0.9409 1.757 0.9359 0.9615 0.8462 0.9295 0.2791 0.3565 0 0.8011 0.00E+00 0.8561 0.00E+00
17 -0.516367649 0.699129856 6041 755 806 9082 312 420 156 728 0 1.659 1.687 1.622 0.9423 1.774 0.9679 0.9744 0.8526 0.8846 0.272 0.3164 0 0.8095 0.00E+00 0.8132 0.00E+00
18 -0.435241609 0.739569888 6302 774 1292 8998 328 555 156 725 0 1.568 1.664 0.9203 0.6925 1.499 0.9423 0.9551 0.8397 0.891 0.2853 0.3415 0 0.7318 0.00E+00 0.7713 0.00E+00
19 0.472947314 1.387942032 4061 774 1320 3085 338 578 156 750 0 0.8357 1.533 0.1306 0.3938 0.1437 1 1 0.9936 0.9936 0.2209 0.1604 0 0.8709 0.00E+00 0.8664 0.00E+00
20 -0.212604351 0.862977977 2768 786 998 3004 340 635 156 722 0 1.344 1.53 0.4844 0.5798 0.7357 0.9936 1 0.9808 1 0.1328 0.151 0 0.8513 0.00E+00 0.8625 0.00E+00

Total number of rows: 16928

Table truncated, full table size 2756 Kbytes.




Supplementary data files not provided

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