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Sample GSM27384 Query DataSets for GSM27384
Status Public on Oct 24, 2004
Title Cotyledon, cn2
Sample type RNA
 
Channel 1
Source name cultured cell
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name cotyledon light
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Cotyledon light vs Cultured cell
 
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, Reference) median pixel intensity
CH2_median Channel 2 (532 nm, Cy3, Experiment) 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 433 310 129 246 447 315 129 60 80 418 5030 10570 100 98 95 55 20 0 0 1 0 .211 -2.2446853 1.000 .211
3203769 213 573 124 229 223 590 79 132 80 408 5380 10740 100 67 35 100 100 0 0 1 0 3.865 1.9504683 1.000 3.865
3205265 202 273 130 220 203 271 63 46 80 418 10580 11990 100 53 23 45 12 0 0 1 -50 .736 -0.4422223 1.000 .736
3205347 192 267 160 258 195 269 75 67 80 418 9350 12340 100 30 13 22 3 0 0 1 -50 .281 -1.8313583 1.000 .281
3206101 143 866 125 183 146 884 52 233 80 399 12590 10980 110 25 2 100 97 0 0 1 0 37.944 5.2458003 1.000 37.944
3206121 142 253 131 199 149 247 59 55 80 386 14330 10990 100 7 0 56 17 0 0 1 -50 4.909 2.2954293 1.000 4.909
3206127 8874 752 128 197 8756 756 2190 193 120 445 14870 11000 120 100 100 99 97 0 0 1 0 .063 -3.9885043 1.000 .063
3206173 261 410 124 203 259 424 88 78 80 451 14690 11170 110 75 65 100 98 0 0 1 0 1.511 0.5955043 1.000 1.511
3206193 414 1336 125 200 412 1285 139 353 120 453 12250 11320 130 94 90 95 94 0 0 1 0 3.931 1.9748963 1.000 3.931
3206207 186 307 135 203 192 314 58 61 80 397 13450 11330 100 37 7 87 62 0 0 1 -50 2.039 1.0278623 1.000 2.039
3206959 870 331 128 180 900 332 243 72 80 426 16640 9920 110 100 100 96 75 0 0 1 0 .204 -2.2933593 1.000 .204
3206971 147 217 131 185 148 219 57 40 80 408 17690 9930 100 23 3 42 11 0 0 1 -50 2.000 1.0000003 1.000 2.000
3206991 181 1862 119 163 190 1757 65 667 120 425 19460 9950 120 54 23 95 95 0 0 1 0 27.403 4.7762623 1.000 27.403
3207003 227 233 129 187 233 231 82 40 80 396 16290 10100 100 57 23 46 11 0 0 1 -50 .469 -1.0923403 1.000 .469
3203713 3078 2507 135 257 3196 2550 1026 621 80 453 4680 10560 110 100 100 100 100 0 0 1 0 .765 -0.3864683 1.000 .765
3203745 2406 813 135 278 2516 857 719 188 80 454 3270 10730 110 100 100 100 100 0 0 1 0 .236 -2.0831413 1.000 .236
3204483 181 320 173 323 196 324 70 80 80 408 9380 9170 100 20 6 16 1 0 0 0 -125 1.000
3204499 313 363 211 295 301 352 90 56 12 104 10760 9200 50 50 0 41 0 0 0 1 0 .667 -0.5842413 1.000 .667
3204567 161 290 137 241 162 296 62 81 80 408 8320 9520 100 21 6 42 13 0 0 1 -50 2.042 1.0299833 1.000 2.042
3205269 288 301 128 188 280 298 120 66 80 498 10940 11990 100 77 62 83 60 0 0 1 0 .706 -0.5022603 1.000 .706

Total number of rows: 27648

Table truncated, full table size 2976 Kbytes.




Supplementary data files not provided
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