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Sample GSM50165 Query DataSets for GSM50165
Status Public on Jan 02, 2006
Title Cell Line_WTA25ng_onePCR
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell line treated with 1nm R1881 for 24 hours, 25ng total RNA WTA one PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name LnCAP_C, prostate cancer cell line treated with ethanol control for 24 hours, 25ng total RNA WTA one PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See the MIAME checklist
 
Submission date May 03, 2005
Last update date May 29, 2005
Contact name Scott Tomlins
E-mail(s) tomlinss@med.umich.edu
Phone 734-615-1417
Organization name University of Michigan
Department Pathology
Lab Chinnaiyan Lab
Street address 1400 E. Medical Center Dr., 5410 CCGC
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL2013
Series (1)
GSE2618 Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

Data table header descriptions
ID_REF
VALUE Median of Ratios (635/532), normalized (lowess window 0.6), log base 2
X the X-coordiante in um of the centor of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in um of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in um of the feature-indicator
F635 Median median feature pixel intensity at wavelength #1 (635nm) (Cy5).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm)
B635 Median the median feature background intensity at wavelength #1 (635 nm).
B635 Mean the mean feature background intesity at wavelength #1 (635 nm).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm).
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD the percentage of feature pixels with intesnsities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of featue pixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm) (Cy3).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm).
B532 Median the median feature background intensity at wavelength #2 (532 nm).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm).
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians (635/532) the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensites, with the median background subtracted.
Mean of Ratios (635/532) the arithmetic mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the standard deviation of pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio.
Rgn R? the coefficient of determnination for the current regression value.
F Pixels the total number of feature pixels
B Pixels the total number of background pixels.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at wavelength #1 with the median background substracted.
F532 Median - B532 the median featue pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at wavelength #2 with the median background subtracted.
Flags the type of flag associated with a feature. Features that could not be identified by Genepix are indicated with -50. Empty spots are indicated with -75.

Data table
ID_REF VALUE X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R? F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
Hs6-1-1-1 -0.498723 840 18400 110 1038 1061 609 307 325 129 76 73 0 1655 1698 1106 455 478 147 76 71 0 0.609 0.607 0.524 0.532 2.233 0.555 0.795 80 541 1931 1997 -0.715 731 1200 754 1243 0
Hs6-1-2-1 -0.243562 1010 18400 110 1696 1606 816 266 279 103 93 88 0 2354 2142 1178 399 412 99 85 82 0 0.731 0.769 0.731 0.781 2.169 0.719 0.874 80 476 3385 3083 -0.451 1430 1955 1340 1743 0
Hs6-1-3-1 null 1190 18390 100 331 371 159 258 274 103 41 22 0 882 906 463 431 442 115 72 63 0 0.162 0.238 0.207 0.19 3.934 0.201 0.201 80 426 524 588 -2.627 73 451 113 475 -50
Hs6-1-4-1 -0.200558 1350 18390 100 850 837 304 278 296 114 90 78 0 1494 1401 520 437 466 160 91 86 0 0.541 0.58 0.607 0.562 1.885 0.562 0.692 80 466 1629 1523 -0.886 572 1057 559 964 0
Hs6-1-5-1 null 1540 18390 70 684 640 190 280 301 117 87 78 0 1511 1319 494 417 459 206 87 84 0 0.369 0.399 0.364 0.327 2.255 0.34 0.56 32 224 1498 1262 -1.437 404 1094 360 902 0
Hs6-1-6-1 -0.110545 1700 18390 100 1397 1500 922 295 306 112 88 81 0 1928 1920 1232 447 452 113 81 77 0 0.744 0.818 0.754 0.749 1.887 0.771 0.886 80 438 2583 2678 -0.426 1102 1481 1205 1473 0
Hs6-1-7-1 0.224578 1880 18390 120 4799 6238 4382 295 317 132 100 99 0 4213 5426 3876 460 474 161 95 91 0 1.2 1.197 1.162 1.273 1.659 1.17 0.952 120 533 8257 10909 0.263 4504 3753 5943 4966 0
Hs6-1-8-1 null 2050 18380 120 882 1016 649 294 311 122 78 70 0 1087 1272 822 426 439 125 75 69 0 0.89 0.853 0.8 0.806 2.169 0.798 0.815 120 526 1249 1568 -0.169 588 661 722 846 0
Hs6-1-9-1 0.46423 2220 18380 120 1840 3423 3240 300 315 127 93 89 0 1528 3115 2934 415 435 132 82 77 0 1.384 1.157 1.131 1.223 1.873 1.129 0.94 120 548 2653 5823 0.468 1540 1113 3123 2700 0
Hs6-1-10-1 null 2400 18380 110 928 971 522 289 321 158 80 71 0 1247 1362 805 404 441 188 77 72 0 0.758 0.712 0.69 0.691 2.229 0.654 0.776 80 503 1482 1640 -0.4 639 843 682 958 0
Hs6-1-11-1 -0.044999 2580 18360 90 851 887 422 275 309 164 82 71 0 1445 1238 606 379 420 218 82 71 0 0.54 0.712 0.678 0.654 2.115 0.627 0.675 52 380 1642 1471 -0.888 576 1066 612 859 0
Hs6-1-12-1 -0.051689 2750 18370 100 1247 1200 636 267 304 181 87 70 0 1526 1561 860 380 417 169 83 78 0 0.855 0.79 0.739 0.816 2.274 0.756 0.812 80 413 2126 2114 -0.226 980 1146 933 1181 0
Hs6-1-13-1 -0.04399 2950 18370 190 1407 1364 385 273 293 136 96 94 0 1827 1749 423 397 424 154 96 94 0 0.793 0.807 0.788 0.768 1.568 0.801 0.827 256 1332 2564 2443 -0.335 1134 1430 1091 1352 0
Hs6-1-14-1 -0.086079 3110 18360 130 1023 1089 605 275 288 111 86 77 0 1458 1496 850 380 400 135 82 79 0 0.694 0.729 0.684 0.597 2.455 0.71 0.843 120 515 1826 1930 -0.527 748 1078 814 1116 0
Hs6-1-15-1 -0.221873 3280 18360 100 877 884 399 263 278 105 95 81 0 1391 1392 641 369 380 100 92 86 0 0.601 0.607 0.599 0.567 1.886 0.595 0.785 80 421 1636 1644 -0.735 614 1022 621 1023 0
Hs6-1-16-1 null 3470 18360 90 509 558 278 266 281 104 73 57 0 1367 1082 625 372 388 103 69 65 0 0.244 0.411 0.394 0.367 2.341 0.353 0.486 52 370 1238 1002 -2.034 243 995 292 710 0
Hs6-1-17-1 -0.091923 3640 18350 100 1378 1436 967 261 280 112 83 73 0 1700 1825 1256 394 410 124 76 73 0 0.855 0.821 0.75 0.655 2.108 0.783 0.883 80 484 2423 2606 -0.226 1117 1306 1175 1431 0
Hs6-1-18-1 null 3820 18350 100 470 468 184 258 269 106 65 48 0 869 841 458 376 392 129 71 63 0 0.43 0.452 0.382 0.455 5.352 0.348 0.455 80 364 705 675 -1.218 212 493 210 465 -50
Hs6-1-19-1 0.152649 3990 18350 190 3127 3039 897 272 285 108 98 98 0 3178 3032 823 401 419 139 96 96 0 1.028 1.052 1.05 1.048 1.36 1.046 0.935 256 1426 5632 5398 0.04 2855 2777 2767 2631 0
Hs6-1-20-1 null 4170 18340 100 358 365 152 265 282 117 42 12 0 399 417 178 372 387 127 26 8 0 3.444 2.222 0.958 1.094 4.046 1.006 0.124 80 396 120 145 1.784 93 27 100 45 -50

Total number of rows: 20000

Table truncated, full table size 3605 Kbytes.




Supplementary data files not provided
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