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Sample GSM27383 Query DataSets for GSM27383
Status Public on Oct 24, 2004
Title Cotyledon, cn1
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 348 235 130 207 367 233 162 54 80 432 4700 10690 110 78 68 30 7 0 0 1 0 .128 -2.9657843 1.000 .128
3203769 217 479 129 196 230 483 96 142 80 453 5040 10870 110 50 21 92 90 0 0 1 0 3.216 1.6852673 1.000 3.216
3205265 209 203 138 174 231 200 76 37 32 224 10260 12110 70 56 25 31 0 0 0 1 0 .408 -1.2933593 1.000 .408
3205347 146 185 122 170 146 185 54 42 80 420 9030 12430 100 28 5 22 8 0 0 1 -50 .625 -0.6780723 1.000 .625
3206101 181 682 129 158 189 692 70 251 80 392 12250 11050 110 48 22 96 95 0 0 1 0 10.077 3.3329943 1.000 10.077
3206121 132 208 120 164 144 209 55 52 80 384 13990 11040 100 7 0 37 8 0 0 1 -50 3.667 1.8746003 1.000 3.667
3206127 7995 841 124 154 8786 826 3871 261 120 401 14530 11060 120 99 99 96 90 0 0 1 0 .087 -3.5228413 1.000 .087
3206173 321 403 120 150 323 428 121 126 80 420 14350 11230 110 90 80 100 98 0 0 1 0 1.259 0.3322783 1.000 1.259
3206193 344 887 127 162 342 964 152 457 156 476 11910 11400 140 83 71 93 91 0 0 1 0 3.341 1.7402803 1.000 3.341
3206207 165 260 116 155 168 253 68 51 80 361 13110 11410 100 5 0 78 60 0 0 1 0 2.143 1.0996323 1.000 2.143
3206959 1122 349 131 161 1169 353 520 99 120 400 16310 9960 120 91 90 93 88 0 0 1 0 .190 -2.3959293 1.000 .190
3206971 147 194 120 167 151 193 65 47 80 402 17350 9960 100 32 13 38 16 0 0 1 -50 1.000 0.0000003 1.000 1.000
3206991 190 2386 124 171 205 2235 89 945 120 455 19120 9960 120 50 27 95 95 0 0 1 0 33.561 5.0687143 1.000 33.561
3207003 254 244 133 159 271 248 79 58 52 360 15960 10140 90 38 3 78 55 0 0 1 0 .702 -0.5104573 1.000 .702
3203713 2958 2293 133 220 3099 2435 1619 986 120 470 4350 10700 120 92 92 99 97 0 0 1 0 .734 -0.4461483 1.000 .734
3203745 3244 1277 139 396 2965 1221 1285 370 120 471 2950 10870 120 95 94 93 90 0 0 1 0 .284 -1.8160373 1.000 .284
3204483 160 207 131 182 173 212 60 53 80 432 9020 9270 100 35 11 25 7 0 0 1 -50 .862 -0.2142403 1.000 .862
3204499 137 272 170 205 148 268 76 74 12 104 10410 9230 50 8 8 75 33 0 0 0 -125 1.000
3204567 160 201 130 182 163 201 62 49 80 408 7970 9620 100 31 10 28 6 0 0 1 -50 .633 -0.6597233 1.000 .633
3205269 156 203 124 171 168 206 80 48 80 452 10600 12080 100 40 18 42 12 0 0 1 -50 1.000 0.0000003 1.000 1.000

Total number of rows: 27648

Table truncated, full table size 2956 Kbytes.




Supplementary data files not provided
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