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Sample GSM13770 Query DataSets for GSM13770
Status Public on Feb 12, 2004
Title KM109 t=0(1) t=6(2) batch II
Sample type RNA
 
Channel 1
Source name KM109 t=0
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name KM109 t=6
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and six days after fusion induction (channel 2, t=6).
 
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 GPL784
Series (1)
GSE909 KM109_Human oligo batch II

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 -0.00151 0.98842 160 191 192 23 168 170 33 28 3 0 305 308 34 236 243 30 92 57 0 0.333 0.333 0.353 0.333 2.35 0.404 0.444 208 1414 92 96 -1.585 23 69 24 72 0 -0.00151
2 -0.01068 0.91497 140 211 216 29 174 177 36 51 14 0 313 318 35 237 246 32 92 61 0 0.487 0.519 0.54 0.463 2.032 1.33 0.34 156 1093 113 123 -1.038 37 76 42 81 0 -0.01068
3 -0.06489 0.51641 170 244 247 44 173 174 16 92 84 0 338 336 48 228 232 24 96 88 0 0.645 0.685 0.683 0.647 1.656 0.711 0.694 208 1490 181 182 -0.632 71 110 74 108 0 -0.06489
4 -0.06528 1 150 200 200 17 172 173 14 77 47 0 290 294 27 226 227 14 99 94 0 0.438 0.412 0.441 0.387 1.931 0.436 0.439 156 1236 92 96 -1.193 28 64 28 68 0 -0.06528
5 -0.12323 0.21784 150 422 470 135 175 176 15 100 100 0 421 457 94 229 230 15 100 100 0 1.286 1.294 1.3 1.268 1.289 1.352 0.884 156 1214 439 523 0.363 247 192 295 228 0 -0.12323
6 -0.11292 0.25882 150 389 417 117 175 176 15 99 99 0 524 548 124 231 232 15 100 100 0 0.73 0.763 0.758 0.723 1.44 0.78 0.873 156 1198 507 559 -0.453 214 293 242 317 0 -0.11292
7 0.48971 200 183 182 16 177 178 17 21 3 0 260 261 20 241 249 38 14 0 0 0.316 0.25 0.588 0.643 3.387 0.204 0.149 316 1852 25 25 -1.663 6 19 5 20 -75 -0.06908
8 0.64022 200 186 187 15 178 178 17 28 5 0 272 274 20 248 257 37 21 0 0 0.333 0.346 0.474 0.496 3.096 0.437 0.123 316 1806 32 35 -1.585 8 24 9 26 -75 -0.04674
9 -0.113 0.25849 190 284 282 29 175 176 16 98 96 0 395 393 25 240 244 21 100 100 0 0.703 0.699 0.69 0.674 1.379 0.728 0.798 256 1622 264 260 -0.508 109 155 107 153 0 -0.113
10 0.06074 0.92129 190 261 258 28 174 174 15 97 94 0 353 351 22 236 237 15 100 100 0 0.744 0.73 0.724 0.702 1.469 0.77 0.747 256 1617 204 199 -0.427 87 117 84 115 0 0.06074
11 -0.10285 0.30373 230 225 222 30 173 173 14 84 74 0 336 328 42 235 236 16 94 89 0 0.515 0.527 0.528 0.517 1.797 0.545 0.671 392 1727 153 142 -0.958 52 101 49 93 0 -0.10285
12 -0.03774 1 200 267 264 34 174 174 16 96 93 0 363 356 35 236 239 21 96 93 0 0.732 0.75 0.76 0.744 1.623 0.772 0.797 316 1660 220 210 -0.45 93 127 90 120 0 -0.03774
13 -0.00855 0.93188 190 267 265 28 174 175 16 98 98 0 362 360 21 235 237 20 100 100 0 0.732 0.728 0.722 0.699 1.399 0.769 0.791 256 1596 220 216 -0.45 93 127 91 125 0 -0.00855
14 0.05239 0.60038 210 274 273 27 181 181 17 99 96 0 369 362 29 240 245 33 97 93 0 0.721 0.754 0.743 0.748 1.375 0.739 0.749 316 1770 222 214 -0.472 93 129 92 122 0 0.05239
15 -0.0344 0.73087 200 268 268 25 190 199 50 89 19 0 350 347 24 243 257 59 95 29 0 0.729 0.75 0.738 0.747 1.526 0.751 0.753 316 1957 185 182 -0.456 78 107 78 104 0 -0.0344
16 -0.082 1 160 286 285 32 167 168 16 99 99 0 414 412 25 240 243 23 100 100 0 0.684 0.686 0.687 0.664 1.345 0.712 0.843 208 1310 293 290 -0.548 119 174 118 172 0 -0.082
17 -0.54658 0.00183 170 337 331 53 166 167 14 99 99 0 426 421 42 227 229 19 100 100 0 0.859 0.851 0.853 0.814 1.439 0.887 0.877 208 1374 370 359 -0.219 171 199 165 194 0 -0.54658
18 -0.29086 0.00363 180 239 238 25 168 170 16 97 92 0 342 335 29 222 227 24 97 95 0 0.592 0.619 0.614 0.597 1.542 0.617 0.735 256 1522 191 183 -0.757 71 120 70 113 0 -0.29086
19 -0.07736 0.43915 170 376 371 44 170 171 15 100 100 0 427 425 30 229 231 22 100 100 0 1.04 1.026 1.023 1.008 1.228 1.043 0.885 208 1367 404 397 0.057 206 198 201 196 0 -0.07736
20 -0.03431 0.73151 190 265 267 25 174 177 25 100 97 0 371 371 24 229 234 34 100 99 0 0.641 0.655 0.639 0.645 1.341 0.638 0.664 256 1636 233 235 -0.642 91 142 93 142 0 -0.03431

Total number of rows: 10800

Table truncated, full table size 1813 Kbytes.




Supplementary data files not provided

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