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Sample GSM27382 Query DataSets for GSM27382
Status Public on Oct 24, 2004
Title Cotyledon, CP2
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
3203713 1955 1389 115 229 2080 1466 663 474 80 507 5130 10710 110 100 100 100 98 0 0 1 0 1.586 0.6653933 1.000 1.586
3203745 724 721 116 224 775 711 393 260 80 452 3740 10870 110 91 88 93 77 0 0 1 0 1.223 0.2904243 1.000 1.223
3204483 161 251 119 248 163 275 73 97 80 486 9830 9290 100 43 13 8 3 0 0 1 -50 14.000 3.8073553 1.000 14.000
3204499 187 319 118 237 194 350 73 136 120 454 11220 9290 120 61 36 46 21 0 0 1 0 .841 -0.2498223 1.000 .841
3204567 148 263 123 236 154 278 66 73 80 430 8800 9640 100 31 17 21 7 0 0 1 0 .926 -0.1109163 1.000 .926
3205269 129 269 131 232 137 329 75 156 32 172 11360 12080 60 18 9 34 15 0 0 0 -125 1.000
3205335 282 368 117 221 304 407 113 141 80 303 8760 12460 110 90 72 60 25 0 0 1 0 1.122 0.1660733 1.000 1.122
3205367 127 248 129 235 138 272 60 99 52 316 7410 12640 80 19 5 9 5 0 0 0 -125 1.000
3206081 634 369 122 240 627 395 291 107 80 452 15500 10910 110 85 63 70 27 0 0 1 0 3.969 1.9887763 1.000 3.969
3206919 167 308 131 265 178 325 78 87 80 406 17800 9830 100 38 18 26 6 0 0 1 -50 .837 -0.2567003 1.000 .837
3206927 324 470 133 266 340 504 105 144 80 467 18500 9840 110 93 83 88 48 0 0 1 0 .936 -0.0954203 1.000 .936
3206963 347 407 135 256 351 440 113 137 80 428 17450 10010 100 91 80 75 35 0 0 1 0 1.404 0.4895433 1.000 1.404
3206989 779 1063 130 275 753 1151 306 443 80 422 19730 10020 100 85 65 100 98 0 0 1 0 .824 -0.2792843 1.000 .824
3207691 659 525 127 257 660 538 235 185 80 358 18140 12640 100 92 76 83 35 0 0 1 0 1.985 0.9891393 1.000 1.985
3203717 113 270 114 225 124 292 51 87 80 418 5480 10690 100 21 3 32 7 0 0 0 -125 1.000
3203769 548 1057 109 215 539 1046 228 274 80 388 5840 10880 110 92 88 98 98 0 0 1 0 .521 -0.9406453 1.000 .521
3205265 160 262 118 223 164 319 57 149 52 347 11050 12090 90 46 19 21 13 0 0 1 0 1.077 0.1070183 1.000 1.077
3205347 171 289 119 226 178 339 69 141 52 340 9820 12490 90 44 17 32 15 0 0 1 0 .825 -0.2775343 1.000 .825
3206101 1344 4838 132 247 1300 5078 646 2092 80 450 13060 11080 110 83 80 92 91 0 0 1 0 .264 -1.9213903 1.000 .264
3206121 292 394 134 246 307 424 128 132 120 490 14800 11090 120 30 5 50 15 0 0 1 0 1.068 0.0949123 1.000 1.068

Total number of rows: 27648

Table truncated, full table size 2961 Kbytes.




Supplementary data files not provided
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