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Sample GSM13769 Query DataSets for GSM13769
Status Public on Feb 12, 2004
Title KM109 t=4(1) t=0(2) batch II
Sample type RNA
 
Channel 1
Source name KM109 t=4
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name KM109 t=0
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 2, t=0) and four days after fusion induction (channel 1, t=4).
 
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 -0.26864 0.00722 180 241 249 39 192 194 27 75 44 0 318 321 34 238 240 24 97 84 0 0.613 0.687 0.672 0.623 1.86 0.94 0.635 256 1630 129 140 -0.707 49 80 57 83 0 -0.26864
2 -0.30801 0.0138 150 234 240 35 193 194 17 77 58 0 312 319 33 240 241 20 98 92 0 0.569 0.595 0.585 0.474 2.339 0.755 0.577 156 1150 113 126 -0.812 41 72 47 79 0 -0.30801
3 -0.38746 0.00011 190 232 234 27 197 199 24 64 29 0 322 322 28 242 243 21 99 89 0 0.438 0.463 0.466 0.4 2.199 0.629 0.405 256 1726 115 117 -1.193 35 80 37 80 0 -0.38746
4 -0.38712 0.00153 170 223 229 38 200 203 27 42 12 0 311 315 27 242 245 32 94 58 0 0.333 0.397 0.407 0.347 2.369 0.661 0.224 208 1422 92 102 -1.585 23 69 29 73 0 -0.38712
5 0.00714 0.94309 190 453 476 159 198 204 90 92 62 0 401 413 76 242 244 49 96 81 0 1.604 1.626 1.552 1.506 1.555 1.784 0.85 256 1666 414 449 0.681 255 159 278 171 0 0.00714
6 0.06831 0.49457 170 602 630 231 198 199 19 100 100 0 439 455 94 245 245 19 100 100 0 2.082 2.057 2.051 1.946 1.316 2.27 0.895 208 1368 598 642 1.058 404 194 432 210 0 0.06831
7 1 200 202 204 17 196 197 18 24 6 0 269 270 20 245 245 18 61 20 0 0.25 0.32 0.558 0.522 3.299 0.476 0.08 316 1761 30 33 -2 6 24 8 25 -75 0.22299
8 1 200 204 210 30 192 193 18 37 17 0 279 301 70 241 243 23 75 35 0 0.316 0.3 0.361 0.352 2.646 0.367 0.497 316 1713 50 78 -1.663 12 38 18 60 -75 0.22299
9 -0.27467 0.00602 210 279 281 28 187 189 18 100 98 0 357 356 22 236 239 27 100 99 0 0.76 0.783 0.78 0.752 1.396 0.797 0.759 316 1649 213 214 -0.395 92 121 94 120 0 -0.27467
10 -0.48252 1.39844E-06 210 241 242 19 186 186 16 98 88 0 367 366 21 240 242 21 99 99 0 0.433 0.444 0.448 0.421 1.559 0.458 0.65 316 1728 182 182 -1.207 55 127 56 126 0 -0.48252
11 -0.59302 3.02553E-09 210 220 220 18 185 186 15 87 57 0 354 355 21 239 239 21 100 100 0 0.304 0.302 0.306 0.275 1.828 0.306 0.495 316 1707 150 151 -1.716 35 115 35 116 0 -0.59302
12 -0.38529 0.00012 230 296 295 37 188 188 17 99 98 0 399 399 30 239 239 20 100 100 0 0.675 0.669 0.661 0.644 1.404 0.699 0.798 392 1741 268 267 -0.567 108 160 107 160 0 -0.38529
13 -0.39007 0.0001 220 260 263 33 196 197 21 93 78 0 363 359 28 241 243 22 99 97 0 0.525 0.568 0.541 0.53 1.631 0.614 0.649 392 1698 186 185 -0.931 64 122 67 118 0 -0.39007
14 -0.36639 0.00025 230 277 281 29 195 197 20 99 95 0 374 375 21 242 243 20 100 100 0 0.621 0.647 0.63 0.617 1.406 0.695 0.742 392 1674 214 219 -0.687 82 132 86 133 0 -0.36639
15 -0.41926 0.00003 230 299 301 35 194 231 159 8 0 0 380 388 45 243 260 70 97 45 0 0.766 0.738 0.742 0.728 1.412 1.048 0.553 392 1917 242 252 -0.384 105 137 107 145 0 -0.41926
16 -0.03936 0.6939 220 510 508 86 192 193 18 100 100 0 412 407 40 235 235 18 99 98 0 1.797 1.837 1.768 1.83 1.353 1.898 0.881 392 1757 495 488 0.845 318 177 316 172 0 -0.03936
17 -0.04318 0.66586 210 443 437 74 193 194 16 100 99 0 394 383 47 238 238 18 98 96 0 1.603 1.683 1.629 1.702 1.433 1.662 0.861 316 1567 406 389 0.68 250 156 244 145 0 -0.04318
18 -0.35088 0.00045 200 267 266 25 196 197 18 99 94 0 350 350 23 239 239 21 100 99 0 0.64 0.631 0.633 0.601 1.518 0.649 0.671 316 1558 182 181 -0.645 71 111 70 111 0 -0.35088
19 -0.21489 0.03164 210 308 308 33 199 201 19 100 99 0 362 359 30 244 244 26 99 97 0 0.924 0.948 0.953 0.941 1.396 0.884 0.722 316 1513 227 224 -0.114 109 118 109 115 0 -0.21489
20 -0.28112 0.00494 220 287 289 26 199 200 18 100 98 0 366 364 27 247 248 26 99 97 0 0.739 0.769 0.762 0.765 1.501 0.744 0.719 392 1405 207 207 -0.435 88 119 90 117 0 -0.28112

Total number of rows: 10800

Table truncated, full table size 1808 Kbytes.




Supplementary data files not provided

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