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Sample GSM21923 Query DataSets for GSM21923
Status Public on Sep 01, 2004
Title Mo17Ch1greenControl2
Sample type RNA
 
Channel 1
Source name Mo17 seedling leaf2and3 control
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name Mo17 seedling leaf2and3 ultraviolet treatment
Organism Zea mays
Extracted molecule total RNA
 
 
Description Inbred lines B73 and Mo17, from the same stocks used to create the IBM mapping lines, were kindly supplied by M. Lee. These lines were increased in the field nursery at Clayton, NC. Individual seeds were placed one per 6 cm pot filled with vermiculite, at a density of 36 pots per flat, and grown in the greenhouse without supplemental lighting for ten days to the two-leaf stage. The greenhouse photosynthetically active radiation levels are ~20% less than outdoor radiation. The two lines were then exposed to 4 h of ultraviolet radiation from UV313 bulbs (Q Panel, Westlake, OH, USA) suspended about 30 cm above the plants. The UV dose was measured at plant height using the UV-B sensor on an International Light radiometer Model IL1400A (International Light, Newburyport, MA); the treatment plants received a total UV dose of 86 Jm-2. Control plants were placed under UV313 bulbs that were covered with polyester (MylarD, US Plastics, Lima, OH, USA), which transmits visible light but excludes UV-B. After UV irradiation the UV bulbs were turned off and the plants were allowed to recover for 4 h in the greenhouse. The second and third seedling leaf from each of four plants was harvested and dropped immediately into liquid nitrogen. Pooling assured sufficient RNA and also decreases biological variability. Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA), as described in the microarray manufacturer’s protocol (http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html#P3). PolyA-plus messenger RNA was prepared from the total RNA using a Qiagen Oligotex kit (Qiagen Corp., Valencia, CA). Poly(A)+ RNA was isolated using Oligotex (Qiagen Inc., Valencia, CA), and 4 mg of poly (A)+ RNA was used for each cDNA synthesis using Superscript II reverse transcriptase (Life Technologies, Carlsbad, CA). cDNA was labeled using 100 mM Cy5-dUTP or Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA). About 95% of the spotted cDNAs showed significant hybridization when leaf mRNA was used for the experiments. The control sample was labeled with Cy3-dUTP fluorescent dye and the UV treatment sample was labeled with Cy5-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA). Two samples, one labeled with each dye, were mixed and then hybridized to a microarray for 15 h at 60°C. The slides were washed in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC. The three washes were at room temperature for 5 min each with gentle shaking. The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA). Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities. Scanalyze (Eisen, http://rana.lbl.gov/EisenSoftware.htm) was used to quantify the image files from the scanner.
Keywords = ultraviolet maize corn seedling leaf
 
Submission date Apr 29, 2004
Last update date May 05, 2009
Contact name Ann Stapleton
E-mail(s) stapletona@uncw.edu
Phone 910 962-7267
Organization name University of North Carolina Wilmington
Department Biological Sciences
Street address 601 S. College
City Wilmington
State/province NC
ZIP/Postal code 29403
Country USA
 
Platform ID GPL1208
Series (1)
GSE1353 splitplotnestedANOVA

Data table header descriptions
ID_REF
GRID print-tip group
CH1_MEAN
CH1_BKD_MED
CH1_BKD_MEAN
CH2_MEAN
CH2_BKD_MED
CH2_BKD_MEAN
SPIX
BGPIX
VALUE Derived by taking the log base 2 of the median of ratios (MRAT). This does not include standardization across all arrays, so these values are not directly comparable to values from other arrays in this experiment.
MRAT
REGR
CORR
LFRAT
CH1GTB1
CH2GTB1
CH1GTB2
CH2GTB2
CH1EDGEA
CH2EDGEA
FLAG
CH1KSD
CH1KSP
CH2KSD
CH2KSP

Data table
ID_REF GRID CH1_MEAN CH1_BKD_MED CH1_BKD_MEAN CH2_MEAN CH2_BKD_MED CH2_BKD_MEAN SPIX BGPIX VALUE MRAT REGR CORR LFRAT CH1GTB1 CH2GTB1 CH1GTB2 CH2GTB2 CH1EDGEA CH2EDGEA FLAG CH1KSD CH1KSP CH2KSD CH2KSP
1 1 311 179 187 368 251 259 156 1156 -0.0412693 0.9718 0.6973 0.6946 1.006 0.6795 0.7372 0.3654 0.4038 0.1155 0.1327 0 0.3541 1.00E-15 0.3251 2.55E-13
2 1 329 182 195 370 246 255 156 955 0.1163653 1.084 0.596 0.7198 0.7704 0.6538 0.7179 0.3205 0.4038 0.1227 0.1316 0 0.2971 6.18E-11 0.3391 4.06E-14
3 1 315 181 200 342 248 259 156 933 -0.1780453 0.8839 0.5496 0.6327 0.8013 0.7115 0.6987 0.391 0.3333 0.1363 0.1418 1 0.3724 6.94E-17 0.275 2.11E-09
4 1 2408 184 200 3077 244 256 156 984 0.3379963 1.264 1.182 0.9256 1.302 0.8718 0.8846 0.6218 0.6859 0.3315 0.3645 0 0.6023 8.41E-44 0.6166 0.00E+00
5 1 2386 183 193 2823 243 251 156 1010 0.3010023 1.232 1.064 0.9317 1.153 0.9103 0.9295 0.6731 0.7821 0.3289 0.3319 0 0.6798 0.00E+00 0.6906 0.00E+00
6 1 2288 178 186 2941 242 248 156 1054 0.3818373 1.303 1.182 0.9295 1.294 0.8974 0.8526 0.609 0.6859 0.3332 0.3161 0 0.6504 0.00E+00 0.623 0.00E+00
7 1 376 177 184 361 239 248 156 1055 -0.4052603 0.7551 0.3594 0.5221 0.5073 0.9231 0.8269 0.6795 0.4615 0.1397 0.1217 0 0.685 0.00E+00 0.4126 5.70E-21
8 1 588 179 188 479 246 257 156 1069 -0.5255383 0.6947 0.5144 0.9278 0.5323 0.8718 0.8013 0.641 0.3974 0.2036 0.1978 0 0.6282 0.00E+00 0.353 1.74E-15
9 1 362 182 192 374 256 266 156 1097 -0.2422943 0.8454 0.55 0.5864 0.8966 0.8462 0.7821 0.6026 0.3974 0.1092 0.1249 0 0.568 1.48E-39 0.3407 1.67E-14
10 1 1405 180 189 1653 254 264 156 1065 0.4146773 1.333 0.9042 0.9107 0.9921 0.8205 0.8205 0.5577 0.5962 0.3213 0.3125 0 0.5478 1.11E-36 0.5088 1.04E-31
11 1 1727 179 183 2072 254 261 156 1029 0.2702303 1.206 0.9034 0.7308 1.334 0.8333 0.8141 0.5769 0.609 0.3391 0.3394 0 0.6185 0.00E+00 0.5492 1.03E-36
12 1 1383 182 185 1918 250 258 156 1035 0.3115033 1.241 1.361 0.8964 1.589 0.8462 0.8077 0.5641 0.6026 0.311 0.3343 0 0.5875 5.70E-42 0.5482 1.33E-36
13 1 2780 183 186 2280 249 254 156 1050 -0.3176063 0.8024 0.7356 0.9442 0.7679 0.9423 0.9423 0.8205 0.8526 0.3305 0.2864 0 0.8255 0.00E+00 0.801 0.00E+00
14 1 2780 184 188 2299 252 266 156 1104 -0.3451983 0.7872 0.7639 0.9571 0.7902 0.9679 0.9551 0.8462 0.8526 0.3155 0.29 0 0.8447 0.00E+00 0.7969 0.00E+00
15 1 2621 186 193 2172 259 273 156 1103 -0.3419033 0.789 0.7757 0.9667 0.7964 0.9038 0.8526 0.7692 0.7628 0.2794 0.2657 0 0.7565 0.00E+00 0.7238 0.00E+00
16 1 297 185 189 320 258 267 156 1009 -0.5766913 0.6705 0.4617 0.4356 1.142 0.7949 0.7244 0.5577 0.2564 0.09688 0.1099 1 0.5576 1.00E-37 0.2604 1.47E-08
17 1 304 185 185 319 263 267 156 1009 -0.4546253 0.7297 0.4545 0.4271 1.157 0.8526 0.6923 0.5705 0.2051 0.1033 0.1188 1 0.6157 0.00E+00 0.2246 1.78E-06
18 1 314 186 194 316 262 270 156 987 -0.8334133 0.5612 0.3667 0.4161 0.741 0.8333 0.6923 0.5962 0.2179 0.112 0.1094 1 0.5975 3.94E-43 0.2138 6.80E-06
19 1 1013 186 200 891 263 277 156 984 -0.3212073 0.8004 0.7119 0.9468 0.7403 0.8205 0.8141 0.6026 0.6603 0.2015 0.1921 0 0.5882 8.53E-42 0.6008 1.39E-43
20 1 946 184 209 851 265 283 156 1010 -0.3584543 0.78 0.7134 0.9249 0.7557 0.8333 0.8141 0.5833 0.6474 0.1933 0.1902 0 0.5586 7.24E-38 0.5764 2.75E-40

Total number of rows: 17296

Table truncated, full table size 2580 Kbytes.




Supplementary data files not provided

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