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Sample GSM73523 Query DataSets for GSM73523
Status Public on Dec 01, 2005
Title 2002-10-11_Slide2_rep3
Sample type RNA
 
Channel 1
Source name common hairy vetch (Vicia villosa)
Organism Vicia villosa
Characteristics collected 28 dap
Extracted molecule total RNA
Extraction protocol Total RNA extracted with Trizol, cleaned with RNeasy (Qiagen)
Label cy5
Label protocol cDNA indirectly coupled with Cy5 monoreactive fluor in 0.05 M sodium bicarbonate, pH 9.0. Labelled cDNA was purified with a QIAquick PCR purification kit and quantified.
 
Channel 2
Source name Vicia pannonica PI 170008
Organism Vicia pannonica
Characteristics collected 42 dap
Extracted molecule total RNA
Extraction protocol Total RNA extracted with Trizol, cleaned with RNeasy (Qiagen)
Label cy3
Label protocol cDNA indirectly coupled with Cy3 monoreactive fluor in 0.05 M sodium bicarbonate, pH 9.0. Labelled cDNA was purified with a QIAquick PCR purification kit and quantified.
 
 
Hybridization protocol The Cy5 and Cy3 labelled cDNAs were combined, and suspended in 45 µl of hybridization buffer (10X SSC and 0.2% SDS) and applied to microarray slides
Scan protocol Fluorescent array images were collected for both Cy5 and Cy3 channels with a GenePix 4000B fluorescent scanner, image intensity data was extracted with Genepix Pro 3.0
Description plant material grown in Metromix-200 growing media in a growth chamber (25C), material collected from top 2.5 cm of tissue on each plant,
plant material immediately placed in cryovials, frozen in liquid N, and stored at -80C until RNA extraction
day of plant material collection corresponds to differing growth rates, such that all plants used in this study were of the same growth
Data processing MA-plots were used to assess for appropriate normalization method
Background subtracted fluorescence intensities transformed to log2 scale were used for statistical analyses
Global normalization model and gene models performed using the Mixed Procedure of SAS
 
Submission date Sep 07, 2005
Last update date Oct 28, 2005
Contact name Kathleen Yeater
E-mail(s) [email protected]
Organization name USDA-ARS
Street address 2150 Centre Avenue
City Fort Collins
State/province CO
ZIP/Postal code 80526
Country USA
 
Platform ID GPL2665
Series (1)
GSE3263 Differential gene expression of Vicia species using a soybean cDNA microarray

Data table header descriptions
ID_REF
F635 Median F635 median fluorescence intensity
F635 Mean F635 mean fluorescence intensity
F635 SD F635 fluorescence intensity standard deviation
B635 Median F635 background median fluorescence intensity
B635 Mean F635 background mean fluorescence intensity
B635 SD F635 background fluorescence intensity standard deviation
% > B635+2SD %of feature pixels greater than two standard deviations
F532 Median F532 median fluorescence intensity
F532 Mean F532 mean fluorescence intensity
F532 SD F532 fluorescence intensity standard deviation
B532 Median F532 background median fluorescence intensity
B532 Mean F532 background mean fluorescence intensity
B532 SD F532 background fluorescence intensity standard deviation
% > B532+2SD %of feature pixels greater than two standard deviations
Ratio of Medians
Ratio of Means
Median of Ratios
Mean of Ratios
F Pixels number of feature pixels
B Pixels number of feature background pixels
Sum of Medians sum of the median of the feature intensities at each wavelength, with median background intensity at each wavelength subtracted
Sum of Means sum of the arithmetic mean of feature intensities at each wavelength, with median background intensity at each wavelength subtracted
VALUE base two logarithm of the ratio of medians (635/532)
F635 Median - B635 635 channel median signal intensity (background subtracted)
F532 Median - B532 532 channel median signal intensity (background subtracted)
F635 Mean - B635 635 channel mean signal intensity (background subtracted)
F532 Mean - B532 532 channel mean signal intensity (background subtracted)
Flags Quality discriminator, ID's with negative values were excluded from statistical analysis

Data table
ID_REF F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+2SD F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+2SD Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1 300 305 114 197 208 87 28 358 359 73 193 199 40 87 0.624 0.651 0.759 0.746 80 463 268 274 -0.68 103 165 108 166 0
2 296 301 101 199 209 89 18 381 385 73 186 195 54 88 0.497 0.513 0.536 0.474 80 441 292 301 -1.007 97 195 102 199 0
3 225 244 113 198 208 90 10 221 226 43 191 197 54 5 0.9 1.314 2.245 2.088 120 638 57 81 -0.152 27 30 46 35 -50
4 217 234 92 201 213 84 10 222 226 48 204 208 50 5 0.889 1.5 1.713 1.862 120 600 34 55 -0.17 16 18 33 22 -50
5 217 237 102 208 218 86 8 232 240 53 202 207 49 15 0.3 0.763 1.449 1.573 120 588 39 67 -1.737 9 30 29 38 -50
6 209 220 94 202 213 162 0 207 213 41 189 194 40 10 0.389 0.75 1.5 1.44 120 648 25 42 -1.363 7 18 18 24 -50
7 462 481 161 198 734 4940 0 376 372 60 185 397 2010 0 1.382 1.513 1.485 1.406 80 467 455 470 0.467 264 191 283 187 0
8 650 673 229 204 211 85 91 461 462 92 189 191 33 98 1.64 1.718 1.685 1.592 80 494 718 742 0.713 446 272 469 273 0
9 238 240 96 193 205 85 15 210 213 41 192 195 54 4 2.5 2.238 2.435 2.505 120 607 63 68 1.322 45 18 47 21 -50
10 231 225 91 195 206 90 3 196 203 38 188 194 57 0 4.5 2 2.788 2.883 120 511 44 45 2.17 36 8 30 15 -50
11 406 406 160 205 211 95 53 285 283 51 193 198 60 32 2.185 2.233 2.123 2.211 52 372 293 291 1.127 201 92 201 90 0
12 341 371 155 211 215 84 36 302 306 44 204 209 49 50 1.327 1.569 1.479 1.263 52 395 228 262 0.408 130 98 160 102 0
13 306 311 120 200 211 92 28 273 279 57 200 206 45 32 1.452 1.405 2.058 1.796 52 315 179 190 0.538 106 73 111 79 0
14 300 307 103 196 208 91 26 273 275 39 188 194 37 63 1.224 1.276 1.462 1.293 52 366 189 198 0.291 104 85 111 87 0
15 314 315 111 201 976 5800 0 258 263 55 191 443 2074 0 1.687 1.583 1.493 1.767 80 457 180 186 0.754 113 67 114 72 0
16 368 368 124 201 209 87 50 287 290 71 191 193 32 71 1.74 1.687 2.124 1.588 80 462 263 266 0.799 167 96 167 99 0
17 275 282 105 209 219 89 12 294 296 50 210 216 44 43 0.786 0.849 1.813 1.311 32 230 150 159 -0.348 66 84 73 86 0
18 215 237 109 207 251 904 0 237 239 43 198 265 1266 0 0.205 0.732 1.625 1.561 120 569 47 71 -2.285 8 39 30 41 -50
19 509 514 199 200 208 87 75 369 366 64 193 197 37 94 1.756 1.815 1.814 1.482 52 379 485 487 0.812 309 176 314 173 0
20 477 475 146 198 215 93 73 406 416 75 196 198 33 100 1.329 1.259 1.286 1.14 52 382 489 497 0.41 279 210 277 220 0

Total number of rows: 312

Table truncated, full table size 34 Kbytes.




Supplementary data files not provided
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