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Sample GSM10318 Query DataSets for GSM10318
Status Public on Oct 29, 2003
Title adult leaf-PE covered leaf in UV-B exposed plants vs PE covered leaf in control plants
Sample type RNA
 
Channel 1
Source name PE covered leaf in UV-B exposed plants
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name PE covered leaf in 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-Bexposed (PE bag)/control (PE bag)
Ratio (J-K)/(M-N) UV-Bexposed (PE bag)/control (PE bag)
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 0.021752911 1.015192215 12704 323 536 7483 351 481 156 1173 0 0.576 0.5689 0.5571 0.9675 0.5663 1 1 1 1 0.1782 0.1864 0 0.9847 0.00E+00 0.9761 0.00E+00
2 0.135308823 1.098327897 12291 331 902 6735 367 674 156 1070 0 0.5324 0.5423 0.528 0.97 0.5353 1 1 1 1 0.1701 0.178 0 0.9497 0.00E+00 0.9202 0.00E+00
3 0.093749091 1.067139729 12748 332 828 7169 365 630 156 1046 0 0.548 0.5525 0.5377 0.9747 0.5441 0.9936 0.9936 0.9936 0.9936 0.1967 0.1952 0 0.9207 0.00E+00 0.9227 0.00E+00
4 -0.112384413 0.925057909 2187 322 466 1527 348 422 156 1009 0 0.6322 0.6248 0.587 0.9207 0.615 0.9295 0.9231 0.8077 0.7756 0.2639 0.2109 0 0.7688 0.00E+00 0.7108 0.00E+00
5 -0.163757746 0.892696858 1965 324 577 1426 351 470 156 1009 0 0.6551 0.6629 0.582 0.9254 0.6075 0.9615 0.9295 0.8718 0.8269 0.2524 0.2128 0 0.7939 0.00E+00 0.7364 0.00E+00
6 -0.142420299 0.905997956 1999 332 607 1436 360 501 156 1009 0 0.6455 0.6464 0.5856 0.9268 0.6109 0.9423 0.8718 0.8013 0.7821 0.2427 0.2008 0 0.6853 0.00E+00 0.6527 0.00E+00
7 -1.254397507 0.419168583 12004 337 581 16656 379 533 156 1009 0 1.395 1.383 1.367 0.974 1.415 0.9744 0.9679 0.9103 0.9038 0.3775 0.3734 0 0.7686 0.00E+00 0.7934 0.00E+00
8 -1.235923957 0.424570501 13792 352 549 18906 394 544 156 1009 0 1.377 1.304 1.333 0.9746 1.379 0.9679 0.9615 0.9103 0.891 0.3591 0.3584 0 0.7919 0.00E+00 0.8145 0.00E+00
9 -1.376269441 0.385213604 11237 357 486 16912 395 484 156 1009 0 1.518 1.483 1.434 0.9603 1.517 1 0.9872 0.9423 0.9551 0.3823 0.3893 0 0.8462 0.00E+00 0.8616 0.00E+00
10 -0.555213651 0.680556266 2745 350 552 2443 385 502 156 1009 0 0.8593 0.8576 0.7879 0.9255 0.8404 0.9744 0.9872 0.9551 0.9487 0.2201 0.2069 0 0.8527 0.00E+00 0.8754 0.00E+00
11 -0.530625814 0.692254382 3010 343 1009 2631 378 759 156 1000 0 0.8448 0.8507 0.6101 0.8848 0.6585 1 1 0.9936 1 0.1851 0.1829 0 0.8516 0.00E+00 0.8916 0.00E+00
12 -0.563148139 0.676823638 2537 338 1411 2275 375 1226 156 1018 0 0.864 0.8445 0.777 0.8864 0.862 0.859 0.8974 0.8141 0.8462 0.2115 0.2093 0 0.6765 0.00E+00 0.7228 0.00E+00
13 -0.736094058 0.600362571 57529 336 1363 56083 373 1331 156 1009 0 0.9741 0.9994 0.9848 0.9865 0.9983 1 0.9936 0.9936 0.9808 0.1728 0.181 0 0.9466 0.00E+00 0.9186 0.00E+00
14 -0.670691519 0.628205501 60024 344 2051 55944 388 1683 156 987 0 0.9309 0.9993 0.9593 0.9773 0.9811 1 1 1 1 0.1426 0.1806 0 0.949 0.00E+00 0.925 0.00E+00
15 -0.731125732 0.602433653 55505 345 2022 53925 380 1568 156 1012 0 0.9707 0.9995 0.9614 0.9839 0.9767 0.9872 1 0.9551 0.9936 0.1877 0.211 0 0.891 0.00E+00 0.9091 0.00E+00
16 0.525052534 1.438985978 10536 339 835 4512 368 643 156 1037 0 0.4064 0.3917 0.4829 0.9057 0.5035 0.9936 0.9551 0.9359 0.8654 0.3373 0.3048 0 0.8519 0.00E+00 0.799 0.00E+00
17 0.560778383 1.475064851 10036 335 395 4212 366 408 156 1009 0 0.3965 0.372 0.404 0.9434 0.4111 0.9744 0.9679 0.9487 0.9038 0.3307 0.2987 0 0.8764 0.00E+00 0.842 0.00E+00
18 0.573971951 1.488616313 9087 338 698 3806 369 553 156 1009 0 0.3928 0.3771 0.387 0.9585 0.3915 0.9936 0.9679 0.9487 0.9295 0.3168 0.282 0 0.8738 0.00E+00 0.8414 0.00E+00
19 -0.022738278 0.984362581 7608 338 874 4685 366 608 156 1009 0 0.5941 0.5867 0.5627 0.9629 0.5734 0.9808 1 0.9359 0.9679 0.1973 0.1879 0 0.8546 0.00E+00 0.8912 0.00E+00
20 0.102336339 1.073510527 7311 339 1010 4168 370 664 156 1000 0 0.5448 0.5462 0.5091 0.9645 0.517 1 1 0.9872 1 0.1806 0.1453 0 0.8812 0.00E+00 0.9176 0.00E+00

Total number of rows: 16928

Table truncated, full table size 2814 Kbytes.




Supplementary data files not provided

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