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Sample GSM27388 Query DataSets for GSM27388
Status Public on Oct 24, 2004
Title Germinating seed, gn1
Sample type RNA
 
Channel 1
Source name Cultured cell
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name germinating seed
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Germinating seed 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 260 423 136 293 261 477 93 203 80 388 4910 10340 100 75 55 50 26 0 0 1 -50 1.048 0.0676393 1.000 1.048
3203769 170 584 134 265 175 626 66 212 80 418 5250 10520 100 37 17 96 71 0 0 1 0 8.861 3.1474703 1.000 8.861
3205265 141 413 139 373 142 445 59 191 80 446 10460 11770 100 15 5 15 5 0 0 1 -50 20.000 4.3219283 1.000 20.000
3205347 170 802 142 356 174 882 60 349 32 236 9240 12110 70 28 9 87 78 0 0 1 0 15.929 3.9935843 1.000 15.929
3206101 141 1879 144 310 150 1942 59 468 80 354 12450 10760 100 17 2 100 100 0 0 0 -125 1.000
3206121 154 426 146 302 163 440 62 136 80 426 14210 10760 100 0 0 42 12 0 0 1 -50 15.500 3.9541963 1.000 15.500
3206127 4996 398 146 276 4928 427 1569 148 120 480 14740 10770 120 99 99 47 13 0 0 1 0 .025 -5.3219283 1.000 .025
3206173 188 651 153 312 188 652 76 157 32 176 14550 10950 60 34 9 87 59 0 0 1 0 9.686 3.2759013 1.000 9.686
3206193 310 620 142 317 329 629 111 178 120 414 12120 11100 120 91 75 75 38 0 0 1 0 1.804 0.8511993 1.000 1.804
3206207 186 895 147 491 184 951 65 336 52 248 13300 11120 80 28 9 76 36 0 0 1 0 10.359 3.3728133 1.000 10.359
3206959 265 578 137 285 255 589 95 211 52 306 16540 9710 80 69 50 71 51 0 0 1 0 2.289 1.1947173 1.000 2.289
3206971 145 325 139 282 154 373 68 167 80 449 17570 9700 100 20 6 31 11 0 0 1 -50 7.167 2.8413693 1.000 7.167
3206991 147 785 137 269 154 811 63 212 120 468 19330 9720 120 20 7 100 99 0 0 1 0 51.600 5.6892993 1.000 51.600
3207003 187 563 145 260 199 557 79 166 52 361 16190 9860 90 40 25 84 57 0 0 1 0 7.214 2.8507993 1.000 7.214
3203713 964 577 132 310 995 635 371 194 80 490 4560 10340 110 100 100 82 46 0 0 1 0 .321 -1.6393553 1.000 .321
3203745 811 543 136 310 817 605 180 259 80 427 3160 10510 100 100 100 66 45 0 0 1 0 .345 -1.5353323 1.000 .345
3204483 129 337 129 234 133 351 47 172 32 212 9220 8990 70 9 0 46 18 0 0 0 -125 1.000
3204499 134 325 132 206 133 379 43 225 32 156 10710 8960 60 9 0 50 31 0 0 1 0 59.500 5.8948183 1.000 59.500
3204567 154 473 134 321 166 524 72 193 32 224 8220 9300 70 28 12 53 31 0 0 1 0 7.600 2.9259993 1.000 7.600
3205269 156 475 132 294 164 510 72 223 80 489 10800 11730 110 31 10 53 31 0 0 1 0 7.542 2.9149473 1.000 7.542

Total number of rows: 27648

Table truncated, full table size 2884 Kbytes.




Supplementary data files not provided
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