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Sample GSM50167 Query DataSets for GSM50167
Status Public on Jan 02, 2006
Title Cell Line_WTA100pg_twoPCR
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell line treated with 1nm R1881 for 24 hours, 100pg total RNA WTA two 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, 100pg total RNA WTA two 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 null 1350 18660 100 382 395 225 127 130 39 81 70 0 812 736 445 142 145 39 83 81 0 0.381 0.451 0.412 0.41 1.589 0.45 0.829 80 458 925 862 -1.394 255 670 268 594 0
Hs6-1-2-1 null 1510 18660 110 686 613 333 129 134 41 87 83 0 817 778 451 147 154 49 87 83 0 0.831 0.767 0.768 0.802 1.885 0.739 0.909 80 506 1227 1115 -0.266 557 670 484 631 0
Hs6-1-3-1 null 1720 18650 50 189 184 42 128 135 43 58 33 0 355 355 51 143 167 89 100 66 0 0.288 0.264 0.33 0.232 2.663 0.12 0.075 12 104 273 268 -1.797 61 212 56 212 0
Hs6-1-4-1 null 1860 18660 110 415 423 173 131 136 47 93 87 0 546 495 228 142 150 48 87 77 0 0.703 0.827 0.809 0.881 2.08 0.792 0.785 80 586 688 645 -0.508 284 404 292 353 0
Hs6-1-5-1 null 2050 18660 60 358 359 140 134 142 56 93 78 0 558 493 188 135 147 57 90 87 0 0.53 0.628 0.628 0.613 1.849 0.634 0.716 32 176 647 583 -0.917 224 423 225 358 0
Hs6-1-6-1 -0.66893 2230 18670 110 726 706 397 129 133 41 90 86 0 1089 1067 665 144 148 37 88 86 0 0.632 0.625 0.606 0.655 2.184 0.598 0.863 80 481 1542 1500 -0.663 597 945 577 923 0
Hs6-1-7-1 -0.254855 2400 18660 130 1975 2630 1921 137 142 48 99 97 0 2336 3110 2194 156 166 52 98 95 0 0.843 0.844 0.837 0.856 1.515 0.853 0.939 120 630 4018 5447 -0.246 1838 2180 2493 2954 0
Hs6-1-8-1 null 2580 18670 120 434 489 255 147 150 50 85 82 0 459 565 311 163 176 61 88 79 0 0.97 0.851 0.808 0.87 1.865 0.825 0.826 120 509 583 744 -0.045 287 296 342 402 0
Hs6-1-9-1 -0.013715 2740 18670 120 1276 1797 1515 149 153 50 99 95 0 1477 1812 1431 166 176 60 95 92 0 0.86 1.001 0.967 0.982 1.758 1.029 0.93 120 515 2438 3294 -0.218 1127 1311 1648 1646 0
Hs6-1-10-1 null 2920 18670 120 491 519 257 149 152 49 86 83 0 539 544 266 167 179 66 85 75 0 0.919 0.981 1.018 1.024 1.566 0.966 0.851 120 516 714 747 -0.121 342 372 370 377 0
Hs6-1-11-1 null 3100 18670 120 416 471 262 141 147 51 80 77 0 412 484 293 156 166 58 80 73 0 1.074 1.006 0.957 0.836 2.342 0.935 0.829 120 572 531 658 0.103 275 256 330 328 0
Hs6-1-12-1 null 3270 18690 80 660 612 294 133 147 59 88 78 0 735 685 365 138 148 51 82 82 0 0.883 0.876 0.778 0.816 1.728 0.815 0.78 52 217 1124 1026 -0.18 527 597 479 547 0
Hs6-1-13-1 0.338829 3460 18670 230 1590 1542 562 139 147 51 98 97 0 1360 1291 433 159 169 60 97 96 0 1.208 1.239 1.24 1.227 1.332 1.255 0.947 392 1770 2652 2535 0.273 1451 1201 1403 1132 0
Hs6-1-14-1 null 3630 18670 80 120 135 48 133 140 47 15 3 0 141 140 43 141 147 46 15 0 0 100000 -2 0.986 1.093 3.051 0.837 0.697 52 199 -13 1 16.61 -13 0 2 -1 -50
Hs6-1-15-1 null 3790 18680 120 569 630 337 133 139 43 94 89 0 764 788 484 150 153 47 90 87 0 0.71 0.779 0.767 0.871 1.861 0.722 0.891 120 521 1050 1135 -0.494 436 614 497 638 0
Hs6-1-16-1 null 3970 18670 100 380 373 147 132 136 42 91 83 0 648 594 248 144 147 41 87 86 0 0.492 0.536 0.502 0.527 2.234 0.518 0.769 80 435 752 691 -1.023 248 504 241 450 0
Hs6-1-17-1 0.02644 4140 18670 100 1846 1715 926 132 136 45 97 93 0 1972 1718 891 143 151 46 92 91 0 0.937 1.005 1.01 1.01 1.566 1.013 0.951 80 470 3543 3158 -0.094 1714 1829 1583 1575 0
Hs6-1-18-1 null 4330 18670 80 368 355 123 132 141 45 88 86 0 529 488 189 138 146 46 88 86 0 0.604 0.637 0.581 0.59 1.477 1.575 0.754 52 244 627 573 -0.728 236 391 223 350 -50
Hs6-1-19-1 0.47694 4490 18670 210 2328 2220 706 148 154 57 98 97 0 1759 1669 496 160 170 57 96 95 0 1.363 1.373 1.385 1.387 1.462 1.411 0.952 316 1594 3779 3581 0.447 2180 1599 2072 1509 0
Hs6-1-20-1 null 4680 18680 80 148 158 54 143 156 80 9 1 0 156 156 56 146 153 58 13 5 0 0.5 1.5 1.145 0.897 4.069 0.885 0.258 52 259 15 25 -1 5 10 15 10 -50

Total number of rows: 20000

Table truncated, full table size 3548 Kbytes.




Supplementary data files not provided
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