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Sample GSM27378 Query DataSets for GSM27378
Status Public on Oct 24, 2004
Title Cauline leaf, p1
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
3203713 665 813 86 185 653 812 278 277 120 481 5060 10300 120 95 92 96 95 0 0 1 0 .922 -0.1171613 1.000 .922
3203745 160 678 84 193 174 696 80 153 80 478 3660 10460 110 71 50 100 100 0 0 1 0 .157 -2.6711643 1.000 .157
3204483 99 189 94 181 101 191 45 52 80 374 9740 8890 100 15 6 21 10 0 0 1 -50 .625 -0.6780723 1.000 .625
3204499 125 198 95 171 128 198 53 43 80 423 11140 8890 100 38 13 36 6 0 0 1 -50 1.111 0.1518593 1.000 1.111
3204567 106 200 91 179 115 207 45 51 80 424 8690 9230 100 30 10 33 12 0 0 1 -50 .714 -0.4860043 1.000 .714
3205269 114 202 92 182 118 208 44 48 80 477 11310 11700 100 32 12 25 11 0 0 1 -50 1.100 0.1375043 1.000 1.100
3205335 143 280 87 180 154 280 63 63 80 440 8690 12050 100 62 41 77 52 0 0 1 0 .560 -0.8365013 1.000 .560
3205367 104 209 90 179 106 213 44 54 80 427 7280 12210 100 30 12 42 16 0 0 1 -50 .467 -1.0985063 1.000 .467
3206081 446 224 81 178 466 222 153 47 80 415 15400 10500 110 100 100 50 16 0 0 1 0 7.935 2.9882303 1.000 7.935
3206919 112 185 95 167 117 195 48 54 80 406 17710 9410 100 28 7 40 15 0 0 1 -50 .944 -0.0831413 1.000 .944
3206927 158 403 89 168 172 400 65 101 80 419 18420 9420 110 75 41 98 92 0 0 1 0 .294 -1.7661123 1.000 .294
3206963 164 215 91 168 174 215 73 50 52 308 17380 9580 80 61 44 55 26 0 0 1 0 1.553 0.6350583 1.000 1.553
3206989 243 292 97 178 251 285 78 58 52 367 19640 9590 90 96 75 86 63 0 0 1 0 1.281 0.3572703 1.000 1.281
3207691 464 219 86 174 485 222 142 47 80 408 18070 12210 100 100 100 51 22 0 0 1 0 8.400 3.0703893 1.000 8.400
3203717 81 270 86 185 98 277 55 63 80 408 5400 10290 100 25 11 68 41 0 0 0 -125 1.000
3203769 220 228 83 191 219 234 68 56 52 358 5760 10490 90 92 82 38 13 0 0 1 0 3.703 1.8886953 1.000 3.703
3205265 94 217 91 180 102 216 38 50 80 472 10960 11700 100 21 2 45 17 0 0 1 -50 .081 -3.6259343 1.000 .081
3205347 113 217 93 182 121 226 52 54 80 420 9730 12040 100 35 16 46 21 0 0 1 -50 .571 -0.8084373 1.000 .571
3206101 1006 194 83 175 1025 196 253 43 80 427 12960 10670 110 100 100 22 2 0 0 1 0 48.579 5.6022613 1.000 48.579
3206121 146 200 89 178 154 207 60 56 80 399 14700 10660 100 0 0 30 3 0 0 1 -50 2.591 1.3735093 1.000 2.591

Total number of rows: 27648

Table truncated, full table size 2932 Kbytes.




Supplementary data files not provided
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