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Sample GSM13756 Query DataSets for GSM13756
Status Public on Feb 12, 2004
Title KM109 t=0(1) t=1(2) batch I
Sample type RNA
 
Channel 1
Source name KM109 t=0
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name KM109 t=1
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Timecourse experiment hybridized to human oligo array part I. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and one day after fusion initiation (channel 2, t=1)
 
Submission date Dec 16, 2003
Last update date Nov 22, 2005
Contact name Ellen Sterrenburg
E-mail(s) E.sterrenburg@lumc.nl
Phone +31 71 527 6611
Organization name Leiden University Medical Center
Department Center for Human and Clinical Genetics
Lab Center for Human and Clinical Genetics
Street address Wassenaarseweg 72
City Leiden
ZIP/Postal code 2333 AL
Country Netherlands
 
Platform ID GPL783
Series (1)
GSE908 KM109_Human oligo batch I

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
P-value P-value of the difference (Rosetta Resolver)
Dia. Diameter of the spot
F1 Median Intensity target sample t=0
F1 Mean Mean signal intensity target sample t0
F1 SD Standard deviation of the intensity
B1 Median Median background of target sample
B1 Mean Mean background of target sample
B1 SD standard deviation of the background
% > B1+1SD Percentage of pixels that have a higher intensity than the background plus 1 SD
% > B1+2SD Percentage of pixels that is higher than the backgound plus 2 SD
F1 % Sat. Percentage saturated pixels
F2 Median Intensity target sample t=0
F2 Mean Mean signal intensity target sample t0
F2 SD Standard deviation of the intensity
B2 Median Background of reference sample
B2 Mean Mean background
B2 SD Standard deviation of the background
% > B2+1SD Percentage of pixels that have a higher signal than the background plus 1 SD
% > B2+2SD Percentage of pixels that have a higher signal than the background plus 2 SD
F2 % Sat. Percentage saturated pixels
Ratio of Medians Ratio of median intensities
Ratio of Means Ratio of mean intensities
Median of Ratios Median of ratios
Mean of Ratios Mean of ratios
Ratios SD Standard deviation
Rgn Ratio Regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn Rē Coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels Number of pixels in the foreground
B Pixels Number of pixels in the background
Sum of Medians Sum of medians
Sum of Means Sum of means
Log Ratio Log ratio
F1 Median - B1 Median intensity of channel 1 minus the local background
F2 Median - B2 Median intensity of channel 2 minus the local background
F1 Mean - B1 Median intensity of target minus the local background
F2 Mean - B2 Median intensity of the reference sample minus the local background
Flags Negative number means the spot is bad or not found
UNF_VALUE normalized log10 ratio of channel 1 divided by channel two (ratio profiles, Rosetta Resolver)

Data table
ID_REF VALUE P-value Dia. F1 Median F1 Mean F1 SD B1 Median B1 Mean B1 SD % > B1+1SD % > B1+2SD F1 % Sat. F2 Median F2 Mean F2 SD B2 Median B2 Mean B2 SD % > B2+1SD % > B2+2SD F2 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn Rē F Pixels B Pixels Sum of Medians Sum of Means Log Ratio F1 Median - B1 F2 Median - B2 F1 Mean - B1 F2 Mean - B2 Flags UNF_VALUE
1 -0.15849 0.11299 180 224 224 25 167 168 16 96 82 0 345 349 36 264 267 34 95 68 0 0.704 0.671 0.707 0.647 1.72 0.452 0.417 256 1628 138 142 -0.507 57 81 57 85 0 -0.15849
2 0.00007 0.99966 140 222 223 32 166 167 16 88 73 0 325 324 34 265 267 28 78 51 0 0.933 0.966 0.994 0.951 2.012 0.822 0.553 156 1060 116 116 -0.1 56 60 57 59 0 0.00007
3 -0.11663 0.26103 170 249 248 36 167 168 19 97 85 0 363 373 47 268 275 44 96 58 0 0.863 0.771 0.791 0.751 1.606 0.563 0.56 208 1466 177 186 -0.212 82 95 81 105 0 -0.11663
4 -0.10613 0.38618 170 214 213 26 165 166 15 87 74 0 327 330 32 264 267 28 86 57 0 0.778 0.727 0.74 0.702 2.069 0.635 0.506 208 1410 112 114 -0.363 49 63 48 66 0 -0.10613
5 0.02065 0.83643 180 487 522 154 169 169 16 100 100 0 475 501 97 271 274 32 100 100 0 1.559 1.535 1.515 1.526 1.282 1.59 0.873 256 1536 522 583 0.64 318 204 353 230 0 0.02065
6 0.08042 0.42125 190 466 487 145 167 167 16 100 100 0 430 436 75 259 262 36 99 94 0 1.749 1.808 1.795 1.801 1.301 1.839 0.843 256 1598 470 497 0.806 299 171 320 177 0 0.08042
7 1 200 184 184 18 170 171 21 32 5 0 278 281 29 262 265 33 24 5 0 0.875 0.737 0.647 0.704 3.358 0.281 0.158 316 1790 30 33 -0.193 14 16 14 19 -75 0.26334
8 1 200 194 197 38 172 173 17 57 29 0 300 304 62 268 268 34 47 14 0 0.688 0.694 0.638 0.594 2.827 0.454 0.43 316 1794 54 61 -0.541 22 32 25 36 -75 0.26334
9 -0.09006 0.3678 190 429 430 42 173 174 18 100 100 0 487 487 40 270 275 43 100 100 0 1.18 1.184 1.152 1.187 1.251 1.138 0.816 256 1584 473 474 0.238 256 217 257 217 0 -0.09006
10 -0.12687 0.20455 190 265 265 27 177 178 18 99 97 0 384 384 26 271 278 38 100 91 0 0.779 0.779 0.767 0.754 1.474 0.77 0.662 256 1621 201 201 -0.361 88 113 88 113 0 -0.12687
11 -0.24646 0.01816 170 224 225 20 182 183 22 81 45 0 353 355 33 272 274 33 96 70 0 0.519 0.518 0.5 0.485 1.866 0.535 0.482 208 1418 123 126 -0.948 42 81 43 83 0 -0.24646
12 -0.13686 0.17113 200 799 796 85 198 200 25 100 100 0 752 754 71 269 272 39 100 100 0 1.244 1.233 1.238 1.229 1.14 1.232 0.936 316 2022 1084 1083 0.315 601 483 598 485 0 -0.13686
13 -0.19525 0.25679 170 221 219 26 193 195 26 50 14 0 328 327 33 267 272 34 75 44 0 0.459 0.433 0.525 0.485 2.35 0.594 0.296 208 1385 89 86 -1.123 28 61 26 60 0 -0.19525
14 -0.12493 0.58716 210 266 277 135 171 174 39 96 68 0 364 383 162 258 264 102 57 2 0 0.896 0.848 0.854 0.832 1.504 0.429 0.326 316 1795 201 231 -0.158 95 106 106 125 0 -0.12493
15 -0.09327 0.351 200 307 306 35 176 200 108 74 0 0 391 393 36 266 279 110 68 1 0 1.048 1.024 1.033 1.017 1.406 0.336 0.272 316 1981 256 257 0.068 131 125 130 127 0 -0.09327
16 0.02584 0.79608 200 1275 1186 260 166 167 16 100 100 0 878 823 145 272 276 35 99 98 0 1.83 1.851 1.833 1.89 1.35 1.88 0.96 316 1732 1715 1571 0.872 1109 606 1020 551 0 0.02584
17 -0.11879 0.23488 190 235 235 24 166 167 17 98 93 0 361 362 26 272 275 28 100 90 0 0.775 0.767 0.772 0.744 1.469 0.68 0.621 256 1563 158 159 -0.367 69 89 69 90 0 -0.11879
18 -0.08532 0.57343 180 227 229 24 166 169 39 83 26 0 353 359 31 273 286 122 9 0 0 0.762 0.733 0.738 0.717 1.593 0.171 0.184 256 1458 141 149 -0.391 61 80 63 86 0 -0.08532
19 -0.27755 0.00551 180 484 460 81 165 167 33 100 100 0 653 628 84 269 275 47 100 100 0 0.831 0.822 0.827 0.811 1.238 0.829 0.923 256 1419 703 654 -0.268 319 384 295 359 0 -0.27755
20 -0.13277 0.18429 190 252 253 24 168 171 48 93 32 0 386 387 29 281 284 48 98 60 0 0.8 0.802 0.815 0.796 1.462 0.77 0.677 256 1539 189 191 -0.322 84 105 85 106 0 -0.13277

Total number of rows: 10800

Table truncated, full table size 1807 Kbytes.




Supplementary data files not provided

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