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Sample GSM27392 Query DataSets for GSM27392
Status Public on Oct 24, 2004
Title Hypocotyl, hldn2
Sample type RNA
 
Channel 1
Source name hypocotyl dark
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name hypocotyl light
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Hypocotyl light vs Hypocotyl 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 1041 640 162 138 1031 699 424 239 80 462 5270 10270 110 100 100 100 100 0 0 1 0 1.751 0.8081793 1.000 1.751
3203745 442 407 155 145 486 461 212 188 80 392 3870 10430 100 92 76 100 98 0 0 1 0 1.095 0.1309313 1.000 1.095
3204483 172 229 178 154 186 221 72 48 80 396 9960 8850 100 18 3 71 50 0 0 0 -125 1.000
3204499 267 252 178 167 273 250 88 49 32 236 11380 8840 70 53 15 68 25 0 0 1 0 1.047 0.0662613 1.000 1.047
3204567 178 187 168 141 185 187 83 38 80 397 8910 9200 100 26 5 62 21 0 0 1 -50 .217 -2.2042333 1.000 .217
3205269 191 184 167 146 217 191 98 43 80 466 11520 11670 100 35 8 51 26 0 0 1 -50 .632 -0.6620043 1.000 .632
3205335 300 357 168 140 325 357 112 95 80 408 8900 12020 100 75 42 98 98 0 0 1 0 .608 -0.7178573 1.000 .608
3205367 214 335 179 139 236 336 106 89 80 432 7500 12200 100 35 15 95 95 0 0 1 0 .179 -2.4819693 1.000 .179
3206081 239 313 175 161 257 317 105 82 80 433 15620 10480 100 45 23 91 82 0 0 1 0 .421 -1.2481083 1.000 .421
3206919 181 209 187 138 189 213 78 38 80 420 17930 9380 100 15 5 91 63 0 0 0 -125 1.000
3206927 291 297 183 141 298 298 106 75 80 472 18640 9400 110 60 26 92 85 0 0 1 0 .692 -0.5311563 1.000 .692
3206963 241 259 173 145 252 273 99 65 80 396 17580 9560 100 45 17 97 81 0 0 1 -50 .596 -0.7466163 1.000 .596
3206989 402 610 187 152 415 623 137 139 80 408 19860 9570 100 88 65 100 98 0 0 1 0 .469 -1.0923403 1.000 .469
3207691 1079 519 171 142 1144 528 416 161 80 384 18280 12190 100 100 100 97 96 0 0 1 0 2.408 1.2678353 1.000 2.408
3203717 327 416 164 143 346 416 131 91 80 453 5620 10270 110 83 56 100 100 0 0 1 0 .597 -0.7441973 1.000 .597
3203769 726 477 163 136 743 478 232 133 80 408 5970 10450 100 100 98 100 98 0 0 1 0 1.651 0.7233403 1.000 1.651
3205265 194 184 171 146 199 186 76 43 80 408 11170 11670 100 21 3 52 37 0 0 1 -50 .605 -0.7249933 1.000 .605
3205347 194 216 167 139 202 207 79 50 80 430 9950 12020 100 8 1 52 2 0 0 1 -50 .351 -1.5104573 1.000 .351
3206101 2612 583 165 138 2693 609 808 139 80 452 13160 10650 110 100 100 100 100 0 0 1 0 5.499 2.4591693 1.000 5.499
3206121 224 360 166 162 232 363 80 83 80 390 14920 10650 100 41 16 93 92 0 0 1 0 .293 -1.7710273 1.000 .293

Total number of rows: 27648

Table truncated, full table size 2968 Kbytes.




Supplementary data files not provided
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