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Sample GSM10340 Query DataSets for GSM10340
Status Public on Oct 29, 2003
Title Reciprocity-8 h low UV-B-2
Sample type RNA
 
Channel 1
Source name control
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name UV-B exposure
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 (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 5139 841 950 3342 1135 1228 177 1261 0 0.5135 0.5314 0.4853 0.8919 0.5101 0.9831 0.9548 0.8644 0.8362 0.2064 0.1469 0 0.8221 0.00E+00 0.7954 0.00E+00
2 -0.655354459 0.537615091 5303 850 950 3552 1158 1258 177 1024 0 0.5376 0.535 0.5066 0.8991 0.5321 0.9887 0.9605 0.9153 0.8531 0.2167 0.1482 0 0.8674 0.00E+00 0.7949 0.00E+00
3 5622 861 1206 3500 1201 1488 177 1054 0 0.4829 0.487 0.4759 0.8412 0.5146 0.9887 0.9831 0.9379 0.8814 0.2194 0.1408 0 0.8648 0.00E+00 0.8074 0.00E+00
4 -0.402012014 0.640818626 11507 855 1288 8021 1195 1519 177 1122 0 0.6408 0.6637 0.5812 0.9372 0.602 0.9944 0.9605 0.9435 0.8983 0.3166 0.2691 0 0.8478 0.00E+00 0.7994 0.00E+00
5 -0.478953766 0.607537865 15049 854 1170 9847 1223 1510 177 1158 0 0.6075 0.6361 0.4931 0.87 0.5257 0.9887 0.9774 0.9153 0.9379 0.2801 0.2335 0 0.8377 0.00E+00 0.8786 0.00E+00
6 -0.368075939 0.656071093 12613 910 1522 8968 1290 1749 177 1092 0 0.6561 0.6434 0.643 0.9437 0.6667 0.9944 0.9887 0.9774 0.8927 0.3196 0.2945 0 0.7955 0.00E+00 0.7431 0.00E+00
7 2153 987 1895 1838 1424 2025 177 1030 0 0.3551 0.4019 0.7142 0.7254 0.9788 0.9718 0.7119 0.8927 0.226 0.1231 0.1194 0 0.5769 5.61E-45 0.2316 1.30E-07
8 2389 980 1774 2042 1427 1918 177 1030 0 0.4365 0.4394 0.7169 0.8086 0.8618 0.9831 0.6836 0.8644 0.2599 0.1636 0.1663 0 0.6271 0.00E+00 0.22 6.59E-07
9 2279 879 1287 1983 1354 1623 177 1029 0 0.4493 0.4039 0.6637 0.7665 0.8291 0.9605 0.7175 0.8927 0.2655 0.1617 0.152 0 0.7259 0.00E+00 0.2812 5.17E-11
10 2.075632252 3.569277948 4412 825 925 14110 1307 1379 177 1101 0 3.569 3.59 3.379 0.9296 3.873 0.9096 0.8757 0.6441 0.6949 0.2717 0.3246 0 0.6512 0.00E+00 0.6415 0.00E+00
11 2.211541853 3.921870376 4177 798 844 14522 1270 1352 177 1070 0 3.922 3.856 3.712 0.9465 4.117 0.8757 0.8983 0.6328 0.7345 0.2589 0.3425 0 0.6399 0.00E+00 0.6868 0.00E+00
12 2.262574996 4.063083451 4348 813 865 15625 1262 1333 177 1140 0 4.063 4.087 3.908 0.951 4.298 0.8983 0.8983 0.6441 0.7006 0.2536 0.328 0 0.6056 0.00E+00 0.6635 0.00E+00
13 3000 828 952 3026 1286 1359 177 1082 0 0.8011 0.7903 0.8072 0.9138 0.8731 0.9831 0.8701 0.6836 0.4802 0.2156 0.2038 0 0.6724 0.00E+00 0.4977 7.64E-34
14 2461 810 969 2662 1281 1379 177 1022 0 0.8365 0.8889 0.8128 0.9049 0.8882 0.9322 0.7627 0.6045 0.4294 0.1952 0.1725 0 0.5934 0.00E+00 0.4237 1.92E-24
15 2322 785 876 2616 1286 1340 177 1014 0 0.8653 0.9269 0.8767 0.9405 0.928 0.9661 0.7458 0.678 0.4463 0.1849 0.1597 0 0.6994 0.00E+00 0.4514 1.17E-27
16 900 783 844 1202 1283 1303 177 999 0 -0.6923 0.8968 0.2043 0.2108 0.8618 0.7514 0.339 0.0904 0.01695 0.07308 0.0833 1 0.2804 6.54E-11 0.1825 7.24E-05
17 970 773 881 1300 1302 1373 177 996 0 -0.01015 0.8569 0.3569 0.3072 1.605 0.8362 0.4576 0.1977 0.0339 0.08303 0.1025 1 0.3921 6.47E-21 0.07862 2.99E-01
18 1029 774 864 1313 1308 1395 174 953 0 0.01961 0.8207 0.4394 0.4034 1.234 0.8678 0.4598 0.1609 0.03448 0.1008 0.1001 1 0.4619 2.86E-28 0.07604 3.50E-01
19 0.205682953 0.976493911 4289 758 775 4710 1262 1308 177 1066 0 0.9765 1.028 0.9132 0.9528 0.9564 0.8983 0.904 0.7797 0.774 0.2711 0.2268 0 0.7544 0.00E+00 0.7299 0.00E+00
20 0.232701359 0.994953743 4339 772 839 4812 1263 1342 177 1090 0 0.995 1.071 0.8937 0.9332 0.9547 0.8475 0.904 0.6893 0.7006 0.2222 0.2069 0 0.6507 0.00E+00 0.6469 0.00E+00

Total number of rows: 17294

Table truncated, full table size 2864 Kbytes.




Supplementary data files not provided
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