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Sample GSM13758 Query DataSets for GSM13758
Status Public on Feb 12, 2004
Title KM109 t=0(1) t=4(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=4
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 four days after fusion initiation (channel 2, 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 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 -0.21085 0.0879 180 219 231 109 176 178 21 84 50 0 357 361 41 274 278 23 95 89 0 0.518 0.632 0.517 0.501 2.013 1.953 0.188 256 1629 126 142 -0.949 43 83 55 87 0 -0.21085
2 -0.24867 0.03375 140 237 238 27 184 185 18 88 74 0 375 378 36 292 291 29 93 82 0 0.639 0.628 0.641 0.61 1.912 0.55 0.613 156 1056 136 140 -0.647 53 83 54 86 0 -0.24867
3 -0.15234 0.12766 180 271 273 35 192 193 18 98 90 0 395 392 36 294 295 24 98 91 0 0.782 0.827 0.823 0.81 1.62 0.827 0.667 256 1578 180 179 -0.354 79 101 81 98 0 -0.15234
4 -0.3219 0.00129 180 232 233 25 199 199 19 73 38 0 375 376 26 299 300 22 99 90 0 0.434 0.442 0.451 0.398 2.188 0.471 0.36 256 1529 109 111 -1.204 33 76 34 77 0 -0.3219
5 0.01709 0.86429 180 625 732 258 200 201 19 99 98 0 543 579 115 297 298 20 100 100 0 1.728 1.887 1.909 1.785 1.501 2.038 0.899 256 1548 671 814 0.789 425 246 532 282 0 0.01709
6 -0.04379 0.66144 180 631 651 180 205 205 18 100 100 0 580 590 103 299 301 19 100 100 0 1.516 1.533 1.538 1.503 1.315 1.594 0.914 256 1515 707 737 0.6 426 281 446 291 0 -0.04379
7 1 200 237 280 523 214 216 23 48 17 0 358 363 54 307 308 26 83 47 0 0.451 1.179 0.532 0.523 2.814 25.369 0.05 316 1717 74 122 -1.149 23 51 66 56 -75 0.31414
8 1 200 246 255 80 227 228 25 41 9 0 354 354 28 314 314 33 63 10 0 0.475 0.7 0.612 0.546 3.06 2.245 0.113 316 1785 59 68 -1.074 19 40 28 40 -75 0.31414
9 -0.09329 0.67769 190 649 649 64 236 302 1580 0 0 0 590 585 47 318 343 508 0 0 0 1.518 1.547 1.519 1.556 1.243 3.402 0.786 256 1530 685 680 0.603 413 272 413 267 0 -0.09329
10 -0.49678 0.61524 190 325 326 27 250 311 1532 0 0 0 433 433 23 325 351 493 0 0 0 0.694 0.704 0.7 0.671 1.515 3.432 0.789 256 1626 183 184 -0.526 75 108 76 108 0 -0.49678
11 -0.04245 0.67121 200 460 460 74 256 258 25 99 99 0 488 482 49 333 334 29 98 96 0 1.316 1.369 1.368 1.376 1.453 1.359 0.828 316 1795 359 353 0.396 204 155 204 149 0 -0.04245
12 -0.14177 0.15627 200 1316 1278 180 265 269 48 100 100 0 1054 1038 84 333 335 25 100 100 0 1.458 1.437 1.459 1.412 1.231 1.474 0.949 316 1762 1772 1718 0.544 1051 721 1013 705 0 -0.14177
13 -0.11661 0.24356 200 386 388 46 266 269 47 95 74 0 456 453 35 332 334 27 98 94 0 0.968 1.008 0.991 0.977 1.628 1.051 0.675 316 1721 244 243 -0.047 120 124 122 121 0 -0.11661
14 -0.20344 0.04192 210 362 364 34 252 254 27 99 96 0 454 455 26 320 322 24 100 100 0 0.821 0.83 0.82 0.805 1.421 0.874 0.71 316 1721 244 247 -0.285 110 134 112 135 0 -0.20344
15 -0.08771 0.38041 200 476 477 48 247 269 120 98 37 0 493 499 41 320 334 78 99 71 0 1.324 1.285 1.292 1.282 1.324 1.286 0.807 316 1896 402 409 0.405 229 173 230 179 0 -0.08771
16 0.13536 0.17586 200 1802 1680 436 178 179 19 100 99 0 879 826 162 275 276 22 99 98 0 2.689 2.726 2.701 2.772 1.531 2.785 0.948 316 1736 2228 2053 1.427 1624 604 1502 551 0 0.13536
17 -0.13801 0.16757 180 271 271 30 182 183 23 98 92 0 385 383 31 281 282 25 98 94 0 0.856 0.873 0.85 0.87 1.543 0.878 0.676 256 1446 193 191 -0.225 89 104 89 102 0 -0.13801
18 -0.24837 0.013 180 256 257 24 188 190 18 98 91 0 395 397 27 291 293 29 100 98 0 0.654 0.651 0.673 0.62 1.575 0.616 0.614 256 1492 172 175 -0.613 68 104 69 106 0 -0.24837
19 -0.30405 0.00236 180 702 683 125 196 197 23 100 99 0 835 813 122 298 300 27 100 100 0 0.942 0.946 0.955 0.935 1.44 0.955 0.931 256 1429 1043 1002 -0.086 506 537 487 515 0 -0.30405
20 -0.07858 0.43199 190 362 367 38 197 199 23 100 100 0 438 437 30 295 297 23 100 100 0 1.154 1.197 1.191 1.192 1.264 1.214 0.837 256 1514 308 312 0.206 165 143 170 142 0 -0.07858

Total number of rows: 10800

Table truncated, full table size 1801 Kbytes.




Supplementary data files not provided
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