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Sample GSM50162 Query DataSets for GSM50162
Status Public on Jan 02, 2006
Title Cell Line_WTA10ng_twoPCR
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell line treated with 1nm R1881 for 24 hours, 10ng 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, 10ng 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 -0.281557 1670 18230 100 1237 1224 587 267 281 94 92 83 0 1929 1887 843 476 490 116 95 91 0 0.668 0.678 0.652 0.609 2.418 0.664 0.876 80 496 3166 3111 -0.582 1237 1929 1224 1887 0
Hs6-1-2-1 -0.234114 1850 18230 100 1821 1761 801 282 292 104 96 91 0 2773 2482 1170 485 514 242 91 85 0 0.673 0.741 0.755 0.746 1.693 0.682 0.843 80 453 4594 4243 -0.571 1821 2773 1761 2482 0
Hs6-1-3-1 null 2030 18230 70 412 440 119 251 268 89 78 40 0 1286 1218 323 454 477 147 93 93 0 0.194 0.247 0.208 0.194 2.118 0.195 0.332 32 230 1698 1658 -2.366 412 1286 440 1218 0
Hs6-1-4-1 null 2190 18230 100 980 949 391 258 271 93 90 87 0 1555 1419 649 452 471 143 85 80 0 0.655 0.715 0.655 0.64 1.734 0.647 0.806 80 509 2535 2368 -0.61 980 1555 949 1419 0
Hs6-1-5-1 null 2380 18230 60 800 771 246 267 285 99 93 87 0 1844 1644 616 481 528 206 87 87 0 0.391 0.433 0.402 0.361 2.115 0.36 0.697 32 176 2644 2415 -1.355 800 1844 771 1644 0
Hs6-1-6-1 0.031343 2540 18230 100 2367 2393 1326 265 280 95 93 93 0 2768 2722 1416 460 471 105 92 91 0 0.911 0.941 0.929 0.847 1.993 0.93 0.894 80 442 5135 5115 -0.134 2367 2768 2393 2722 0
Hs6-1-7-1 0.061804 2720 18220 110 9807 9836 5718 290 315 127 100 100 0 9093 8747 4569 480 511 168 100 98 0 1.105 1.155 1.125 1.084 1.541 1.184 0.939 80 511 18900 18583 0.144 9807 9093 9836 8747 0
Hs6-1-8-1 0.332548 2890 18230 100 1563 1584 865 337 359 139 90 86 0 1675 1803 851 553 581 178 90 83 0 1.093 0.998 1.006 1.031 2.799 0.988 0.857 80 440 3238 3387 0.128 1563 1675 1584 1803 0
Hs6-1-9-1 0.138726 3060 18230 100 5068 5716 4080 338 365 145 96 95 0 4876 5451 3304 531 568 188 93 90 0 1.089 1.093 1.107 1.063 2.024 1.154 0.929 80 467 9944 11167 0.123 5068 4876 5716 5451 0
Hs6-1-10-1 0.153109 3260 18230 90 1415 1380 543 287 310 123 94 88 0 1871 1643 638 472 512 277 86 84 0 0.806 0.933 0.893 0.889 1.541 0.873 0.82 52 356 3286 3023 -0.311 1415 1871 1380 1643 0
Hs6-1-11-1 null 3420 18230 100 1100 1159 578 274 287 103 93 87 0 1402 1373 635 464 471 119 86 80 0 0.881 0.974 0.978 0.985 1.894 0.934 0.844 80 428 2502 2532 -0.183 1100 1402 1159 1373 0
Hs6-1-12-1 -0.005874 3580 18220 90 1585 1476 656 262 280 106 94 94 0 2133 1944 839 482 490 118 92 90 0 0.801 0.83 0.835 0.831 1.664 0.808 0.859 52 316 3718 3420 -0.32 1585 2133 1476 1944 0
Hs6-1-13-1 -0.026528 3760 18220 170 1524 1472 393 278 294 116 97 95 0 2037 1961 452 497 517 136 98 96 0 0.809 0.816 0.811 0.811 1.386 0.802 0.867 208 963 3561 3433 -0.306 1524 2037 1472 1961 0
Hs6-1-14-1 0.015911 3940 18230 90 3086 2750 1682 272 293 132 92 88 0 3496 2930 1551 500 512 121 86 86 0 0.939 1.02 0.959 0.97 2.819 1.021 0.899 52 343 6582 5680 -0.091 3086 3496 2750 2930 0
Hs6-1-15-1 0.062868 4120 18240 80 1479 1352 675 283 296 96 90 90 0 1990 1813 930 515 525 106 90 84 0 0.811 0.824 0.855 0.825 1.671 0.737 0.821 52 308 3469 3165 -0.302 1479 1990 1352 1813 0
Hs6-1-16-1 null 4300 18220 90 784 758 296 274 312 342 69 26 0 1660 1453 555 512 597 943 63 0 0 0.444 0.514 0.51 0.484 1.832 0.463 0.716 52 371 2444 2211 -1.171 784 1660 758 1453 0
Hs6-1-17-1 0.010582 4460 18210 90 3524 3067 1571 305 319 113 94 92 0 3994 3327 1630 528 551 147 90 88 0 0.929 0.987 0.975 0.927 1.778 0.978 0.886 52 393 7518 6394 -0.106 3524 3994 3067 3327 0
Hs6-1-18-1 null 4650 18210 60 738 722 191 292 296 95 96 87 0 1443 1304 396 485 513 139 87 87 0 0.466 0.525 0.463 0.506 1.604 0.457 0.597 32 164 2181 2026 -1.102 738 1443 722 1304 0
Hs6-1-19-1 0.076466 4820 18220 170 3111 2966 821 317 338 146 98 98 0 3381 3197 802 537 570 224 96 96 0 0.982 0.996 0.998 0.983 1.393 0.996 0.926 208 1058 6492 6163 -0.026 3111 3381 2966 3197 0
Hs6-1-20-1 null 5000 18220 100 1595 2114 1365 319 331 123 93 88 0 2701 2615 1458 517 540 197 88 82 0 0.584 0.856 0.873 0.782 2.026 0.856 0.907 80 421 4296 4729 -0.776 1595 2701 2114 2615 -50

Total number of rows: 20000

Table truncated, full table size 3675 Kbytes.




Supplementary data files not provided
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