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Sample GSM27380 Query DataSets for GSM27380
Status Public on Oct 24, 2004
Title Cauline leaf, p3
Sample type RNA
 
Channel 1
Source name Cauline leaf
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Cultured cell
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Cauline leaf 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, 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
3203717 99 399 91 229 102 403 45 88 80 480 5480 10340 110 18 6 93 83 0 0 1 0 .047 -4.4111953 1.000 .047
3203769 350 311 90 228 357 313 142 48 80 442 5820 10520 100 95 88 77 37 0 0 1 0 3.133 1.6475453 1.000 3.133
3205265 103 268 90 220 113 284 49 76 80 430 11020 11750 100 36 17 55 32 0 0 1 -50 .271 -1.8836353 1.000 .271
3205347 98 259 89 228 107 258 46 56 80 432 9800 12100 100 28 10 36 13 0 0 1 -50 .290 -1.7858753 1.000 .290
3206101 549 252 95 219 586 253 255 44 80 452 13030 10720 110 92 91 22 1 0 0 1 0 13.758 3.7821993 1.000 13.758
3206121 166 269 105 214 184 269 76 56 32 170 14770 10710 60 59 34 40 15 0 0 1 0 1.109 0.1492593 1.000 1.109
3206127 498 3674 98 216 476 3683 194 1181 80 417 15300 10720 110 93 90 100 100 0 0 1 0 .116 -3.1078033 1.000 .116
3206173 356 309 96 221 333 307 133 60 80 392 15140 10900 100 87 82 73 37 0 0 1 0 2.955 1.5631583 1.000 2.955
3206193 771 382 90 213 824 387 268 78 120 444 12680 11080 130 100 100 96 89 0 0 1 0 4.030 2.0107803 1.000 4.030
3206207 209 271 94 213 222 269 88 52 80 419 13900 11080 110 85 68 57 26 0 0 1 0 1.983 0.9876853 1.000 1.983
3206959 289 643 101 212 279 636 98 114 80 398 17090 9640 110 90 82 100 100 0 0 1 0 .436 -1.1976003 1.000 .436
3206971 106 256 99 234 111 255 39 53 80 464 18130 9640 100 15 5 31 6 0 0 1 -50 .318 -1.6529013 1.000 .318
3206991 2910 328 104 252 2935 332 1011 56 80 408 19890 9650 100 98 98 72 36 0 0 1 0 36.921 5.2063703 1.000 36.921
3207003 169 296 99 211 178 303 67 47 52 350 16750 9820 90 65 40 86 40 0 0 1 0 .824 -0.2792843 1.000 .824
3203713 1839 1673 95 232 1935 1889 584 570 80 464 5120 10350 110 100 100 100 100 0 0 1 0 1.210 0.2750073 1.000 1.210
3203745 385 1773 95 231 398 1695 177 594 80 425 3720 10510 110 93 86 97 93 0 0 1 0 .188 -2.4111953 1.000 .188
3204483 98 253 85 214 104 250 43 46 80 408 9810 8930 100 32 12 45 7 0 0 1 -50 .333 -1.5864063 1.000 .333
3204499 147 293 89 205 161 298 68 59 80 432 11220 8930 100 43 16 75 48 0 0 1 0 .659 -0.6016503 1.000 .659
3204567 108 223 87 222 110 228 47 41 80 408 8760 9280 100 32 8 13 2 0 0 1 -50 21.000 4.3923173 1.000 21.000
3205269 109 229 93 217 110 230 44 50 80 452 11370 11750 100 28 8 23 7 0 0 1 -50 1.333 0.4146773 1.000 1.333

Total number of rows: 27648

Table truncated, full table size 2914 Kbytes.




Supplementary data files not provided
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