NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM21917 Query DataSets for GSM21917
Status Public on Sep 01, 2004
Title B73Ch1greencontrol1
Sample type RNA
 
Channel 1
Source name B73 seedling leaf2and3 control
Organism Zea mays
Extracted molecule total RNA
 
Channel 2
Source name B73 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 experimental UV-treated sample 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.
 
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 1 962 286 289 714 284 293 156 1174 -0.5380523 0.6887 0.6312 0.9211 0.6645 0.7756 0.7179 0.5256 0.5385 0.2253 0.2253 0 0.5283 1.52E-34 0.4604 2.42E-26
2 1 1003 288 312 772 290 304 156 980 -0.5014433 0.7064 0.6366 0.9429 0.6601 0.7115 0.6859 0.4167 0.4679 0.2183 0.2402 0 0.4104 1.50E-20 0.3996 1.64E-19
3 1 990 293 446 735 301 390 156 958 -0.6266023 0.6477 0.617 0.9506 0.6355 0.7372 0.7372 0.4038 0.4167 0.197 0.2026 0 0.3336 1.10E-13 0.3044 1.83E-11
4 1 4679 295 514 4660 301 435 156 984 0.0172093 1.012 0.9705 0.9761 0.9941 0.8462 0.8397 0.6218 0.6987 0.3425 0.3709 0 0.5679 5.37E-39 0.5747 6.32E-40
5 1 4604 293 443 4717 296 391 156 1010 0.0496313 1.035 0.9836 0.9753 1.009 0.8205 0.8462 0.6474 0.7179 0.3567 0.3695 0 0.5904 2.94E-42 0.6042 3.08E-44
6 1 4741 284 355 4811 284 341 156 1046 0.0313953 1.022 0.9944 0.9775 1.018 0.8846 0.8846 0.6859 0.7244 0.3809 0.3719 0 0.6651 0.00E+00 0.6179 0.00E+00
7 1 1382 281 344 1024 285 332 156 1035 -0.5797063 0.6691 0.669 0.9563 0.6887 0.8333 0.8333 0.6346 0.6538 0.184 0.1968 0 0.5998 9.67E-44 0.5835 2.06E-41
8 1 1990 279 422 1556 290 420 156 1048 -0.4994023 0.7074 0.7684 0.9076 0.8325 0.8974 0.8269 0.7051 0.6987 0.2133 0.2172 0 0.6355 0.00E+00 0.6091 4.20E-45
9 1 2485 285 438 1792 288 429 156 1104 -0.4813643 0.7163 0.6542 0.9255 0.6883 0.8846 0.8462 0.7051 0.7244 0.2262 0.2267 0 0.6398 0.00E+00 0.6279 0.00E+00
10 1 6848 291 375 1806 290 357 156 1098 -2.0709673 0.238 0.2326 0.9557 0.2337 0.8397 0.7564 0.5641 0.5385 0.3948 0.323 0 0.5608 1.45E-38 0.4163 1.92E-21
11 1 6122 296 308 1601 293 302 156 1042 -2.0679393 0.2385 0.2254 0.9821 0.2258 0.8141 0.7564 0.6026 0.5321 0.3932 0.305 0 0.595 4.47E-43 0.4461 2.13E-24
12 1 7910 304 309 3277 286 294 156 1020 -1.7216583 0.3032 0.499 0.8847 0.5279 0.9038 0.7692 0.5769 0.5321 0.4139 0.3664 0 0.6179 0.00E+00 0.4693 6.87E-27
13 1 5645 308 311 2838 291 299 156 1017 -1.1668273 0.4454 0.5647 0.9644 0.5751 0.9487 0.9423 0.8462 0.8462 0.3678 0.3248 0 0.8457 0.00E+00 0.8018 0.00E+00
14 1 5293 309 329 2495 291 305 156 1071 -1.1600403 0.4475 0.4362 0.9781 0.4394 0.9487 0.9615 0.8718 0.8654 0.3278 0.2936 0 0.8567 0.00E+00 0.8308 0.00E+00
15 1 4914 308 333 2268 289 309 156 1070 -1.1969383 0.4362 0.4204 0.9695 0.4245 0.9038 0.8654 0.8013 0.7949 0.3005 0.272 0 0.776 0.00E+00 0.7552 0.00E+00
16 1 595 311 324 419 295 312 156 1009 -1.0688463 0.4767 0.4997 0.657 0.6636 0.7885 0.7692 0.609 0.4231 0.1299 0.1367 0 0.5954 5.90E-43 0.3755 2.43E-17
17 1 609 311 331 416 294 312 156 1009 -1.1893513 0.4385 0.4688 0.6386 0.6226 0.8077 0.7436 0.5962 0.4231 0.1351 0.1243 0 0.5841 2.34E-41 0.3629 3.15E-16
18 1 601 305 318 398 284 295 156 987 -1.2976083 0.4068 0.3436 0.597 0.4221 0.7821 0.7564 0.6026 0.4038 0.1216 0.118 0 0.5799 1.17E-40 0.3527 2.61E-15
19 1 2951 300 304 1435 280 287 156 984 -1.1456053 0.452 0.426 0.9696 0.4302 0.8846 0.8462 0.6923 0.6987 0.3371 0.278 0 0.6861 0.00E+00 0.6538 0.00E+00
20 1 2821 294 301 1362 282 289 156 1010 -1.2446853 0.422 0.4193 0.9675 0.4236 0.8782 0.8333 0.7051 0.6923 0.3053 0.2725 0 0.7021 0.00E+00 0.6371 0.00E+00

Total number of rows: 17296

Table truncated, full table size 2563 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap