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Sample GSM27381 Query DataSets for GSM27381
Status Public on Oct 24, 2004
Title Cotyledon, CP1
Sample type RNA
 
Channel 1
Source name Cotyledon light
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Cotyledon dark
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Cotyledon light vs Cotyledon dark
 
Submission date Jul 26, 2004
Last update date May 27, 2005
Contact name Ligeng Ma
E-mail(s) ligeng.ma@yale.edu
Phone 203-432-8909
Organization name Yale University
Department Molecular, Cellular & Developmental Biology
Lab Deng Lab
Street address 165 Prospect
City NEW HAVEN
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL988
Series (1)
GSE1599 Arabidopsis Transcriptome

Data table header descriptions
ID_REF
CH1_median Channel 1 (635 nm, Cy5, Experiment) median pixel intensity
CH2_median Channel 2 (532 nm, Cy3, Reference) median pixel intensity
CH1_back Channel 1 Background
CH2_back Channel 2 Background
CH1_MEAN Channel 1 Mean
CH2_MEAN
CH1_SD Channel 1 Standard Deviation
CH2_SD Channel 2 Standard Deviation
pixels Number of pixels used to determine signal.
bpixels Number of pixels used to determine background.
x X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
diameter diameter in īm of the feature-indicator
%>CH1_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 1
%>CH1_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 1
%>CH2_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 2
%>CH2_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 2
CH1_%Sat percentage of pixel saturation within feature for Channel 1
CH2_%Sat percentage of pixel saturation within feature for Channel 2
QUALITY
flag An extension of GenePix 3.0 flags described at http://twiki.med.yale.edu/twiki/bin/view/YMD/YMDFlagFields
ratio_calc (CH1_median-CH1_back)/(CH2_median-CH2_back)
VALUE log ratio (log2 of PRE_VALUE)
norm_factor Normalization factor calculated as described at http://twiki.med.yale.edu/twiki/bin/view/YMD/NormalizationAndFilterMethods
PRE_VALUE [(Experiment channel median intensity - background)/(Reference channel median intensity - background)]*(norm_factor)

Data table
ID_REF CH1_median CH2_median CH1_back CH2_back CH1_MEAN CH2_MEAN CH1_SD CH2_SD pixels bpixels x y diameter %>CH1_back+1SD %>CH1_back+2SD %>CH2_back+1SD %>CH2_back+2SD CH1_%Sat CH2_%Sat QUALITY flag ratio_calc VALUE norm_factor PRE_VALUE
3203717 178 347 165 274 191 344 86 62 80 390 5510 10420 100 21 7 51 15 0 0 1 -50 .178 -2.4900513 1.000 .178
3203769 602 977 158 277 645 996 255 226 80 452 5860 10600 110 96 95 100 100 0 0 1 0 .634 -0.6574453 1.000 .634
3205265 226 346 170 309 238 354 104 64 80 430 11050 11840 100 40 17 28 6 0 0 1 -50 1.514 0.5983653 1.000 1.514
3205347 308 365 197 307 293 366 90 41 12 104 9800 12200 50 50 8 50 0 0 0 1 0 1.914 0.9365913 1.000 1.914
3206101 876 2390 168 243 870 2411 405 955 120 440 13070 10820 120 88 81 100 99 0 0 1 0 .330 -1.5994623 1.000 .330
3206121 370 365 172 253 354 378 138 64 80 413 14820 10830 110 77 55 92 62 0 0 1 0 1.768 0.8221183 1.000 1.768
3206127 1890 2032 170 256 1894 2023 677 506 120 480 15340 10830 120 98 98 100 100 0 0 1 0 .968 -0.0469213 1.000 .968
3206173 405 703 174 256 411 707 158 151 80 451 15180 11010 110 75 55 98 98 0 0 1 0 .517 -0.9517643 1.000 .517
3206193 962 844 176 250 987 849 391 242 156 477 12730 11170 140 96 95 100 99 0 0 1 0 1.323 0.4038133 1.000 1.323
3206207 291 379 174 247 317 399 121 81 52 281 13930 11190 80 65 28 82 48 0 0 1 0 .886 -0.1746213 1.000 .886
3206959 378 600 180 258 394 613 167 113 120 453 17140 9750 120 77 52 100 100 0 0 1 0 .579 -0.7883653 1.000 .579
3206971 192 315 176 268 214 325 105 64 80 396 18180 9750 100 30 10 48 26 0 0 1 -50 .340 -1.5563933 1.000 .340
3206991 4331 3835 186 267 4357 3584 896 1049 120 458 19930 9770 130 100 100 99 99 0 0 1 0 1.162 0.2166103 1.000 1.162
3207003 393 390 168 254 381 393 129 81 80 446 16780 9920 110 80 65 82 70 0 0 1 0 1.654 0.7259593 1.000 1.654
3203713 2127 1200 167 276 2031 1245 1006 407 120 463 5170 10430 120 96 94 99 98 0 0 1 0 2.121 1.0847453 1.000 2.121
3203745 641 682 150 280 660 713 222 155 80 434 3760 10600 110 98 95 100 100 0 0 1 0 1.221 0.2880633 1.000 1.221
3204483 210 313 173 263 226 315 96 60 80 401 9860 9030 100 31 15 48 12 0 0 1 -50 .740 -0.4344033 1.000 .740
3204499 308 402 173 253 329 406 142 76 80 449 11250 9040 110 67 48 97 73 0 0 1 0 .906 -0.1424173 1.000 .906
3204567 280 379 180 267 298 384 116 74 32 236 8820 9380 70 56 28 87 53 0 0 1 0 .893 -0.1632683 1.000 .893
3205269 216 299 171 285 238 306 104 60 80 480 11400 11850 100 32 17 23 2 0 0 1 -50 3.214 1.6843703 1.000 3.214

Total number of rows: 27648

Table truncated, full table size 2971 Kbytes.




Supplementary data files not provided
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