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Sample GSM27385 Query DataSets for GSM27385
Status Public on Oct 24, 2004
Title Cotyledon dark, n1
Sample type RNA
 
Channel 1
Source name cultured cell
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Cotyledon dark
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Cotyledon dark 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
3203713 1254 744 135 259 1299 802 367 204 80 466 5190 10400 110 100 100 100 100 0 0 1 0 .433 -1.2075613 1.000 .433
3203745 1188 507 135 265 1259 526 424 107 80 406 3790 10570 100 100 100 100 97 0 0 1 0 .230 -2.1202943 1.000 .230
3204483 133 225 136 207 146 224 72 42 80 408 9880 8990 100 15 7 26 3 0 0 0 -125 1.000
3204499 177 231 134 201 176 245 74 54 80 408 11270 8990 100 37 8 41 21 0 0 1 -50 .698 -0.5187013 1.000 .698
3204567 148 219 128 195 148 222 69 42 80 408 8830 9340 100 18 6 35 10 0 0 1 -50 1.200 0.2630343 1.000 1.200
3205269 156 215 136 204 166 224 78 47 80 452 11440 11800 100 28 10 28 12 0 0 1 -50 .550 -0.8624963 1.000 .550
3205335 192 270 135 206 200 276 99 64 52 300 8810 12150 80 46 21 57 32 0 0 1 0 1.123 0.1673583 1.000 1.123
3205367 147 247 130 223 156 249 78 48 80 442 7430 12320 100 22 10 35 10 0 0 1 -50 1.412 0.4977403 1.000 1.412
3206081 165 279 148 216 176 285 68 60 80 389 15540 10590 100 27 3 68 40 0 0 1 -50 3.706 1.8898633 1.000 3.706
3206919 139 231 138 206 150 235 74 51 80 403 17850 9510 100 16 5 35 8 0 0 1 -50 25.000 4.6438563 1.000 25.000
3206927 509 298 140 207 536 317 156 80 80 446 18560 9510 110 100 97 76 50 0 0 1 0 .247 -2.0174173 1.000 .247
3206963 203 277 133 210 207 292 87 66 80 394 17500 9680 100 50 18 70 37 0 0 1 -50 .957 -0.0634093 1.000 .957
3206989 287 376 158 214 300 414 116 156 80 441 19790 9700 100 63 26 88 76 0 0 1 0 1.256 0.3288363 1.000 1.256
3207691 187 304 140 203 194 306 83 65 52 363 18200 12310 90 42 13 82 59 0 0 1 0 2.149 1.1036653 1.000 2.149
3203717 205 294 143 255 223 293 94 46 80 418 5540 10390 100 46 25 46 10 0 0 1 -50 .629 -0.6688683 1.000 .629
3203769 156 619 132 254 169 628 67 120 80 451 5900 10580 110 32 10 98 98 0 0 1 0 15.208 3.9267593 1.000 15.208
3205265 180 224 130 209 185 232 84 49 80 427 11090 11800 100 35 15 28 10 0 0 1 -50 .300 -1.7369663 1.000 .300
3205347 165 244 141 218 164 246 71 54 80 427 9870 12150 100 22 6 31 13 0 0 1 -50 1.083 0.1150333 1.000 1.083
3206101 145 1904 148 227 165 1929 87 495 80 454 13100 10770 110 28 10 100 100 0 0 0 -125 1.000
3206121 158 281 145 219 163 286 71 57 120 483 14840 10770 120 5 0 58 34 0 0 1 0 4.769 2.2536873 1.000 4.769

Total number of rows: 27648

Table truncated, full table size 2917 Kbytes.




Supplementary data files not provided
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