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Sample GSM50133 Query DataSets for GSM50133
Status Public on Jan 02, 2006
Title Cell Line_Unamp
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell lines treated with 1nm synthetic androgen R1881 for 24 hours, 30ug unamplified total RNA, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name LnCAP_C, prostate cancer cell lines treated with ethanol control for 24 hours, 30ug unamplified total RNA, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Please 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 Normalized (lowess window 0.6), log base 2
X the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm 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 µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm) (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 intensity 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 intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature 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 intensities, 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 determination 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 subtracted.
F532 Median - B532 the median feature 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 1630 18420 100 373 375 153 216 468 1415 0 0 0 368 370 138 141 322 973 0 0 0 0.692 0.694 0.694 0.772 2.83 1.695 0.789 80 470 384 388 -0.532 157 227 159 229 0
Hs6-1-2-1 null 1790 18420 100 659 629 283 199 199 28 93 87 0 786 739 377 133 136 21 95 92 0 0.704 0.71 0.7 0.691 1.685 0.717 0.911 80 457 1113 1036 -0.505 460 653 430 606 0
Hs6-1-3-1 null 1980 18430 80 213 189 64 189 198 103 3 0 0 234 206 74 132 140 65 67 17 0 0.235 0 0.381 0.579 3.573 0.548 0.239 52 286 126 74 -2.087 24 102 0 74 0
Hs6-1-4-1 null 2130 18420 110 301 285 121 190 255 485 0 0 0 335 296 118 134 188 421 0 0 0 0.552 0.586 0.759 0.81 2.737 1.217 0.544 80 538 312 257 -0.857 111 201 95 162 0
Hs6-1-5-1 null 2330 18430 80 303 279 108 199 271 558 0 0 0 308 281 120 134 188 411 0 0 0 0.598 0.544 0.657 0.722 2.296 10.935 0.072 52 306 278 227 -0.743 104 174 80 147 0
Hs6-1-6-1 -0.245707 2490 18430 100 732 708 352 198 200 30 85 85 0 793 818 445 134 137 29 92 90 0 0.81 0.746 0.748 0.913 2.002 0.747 0.873 80 414 1193 1194 -0.303 534 659 510 684 0
Hs6-1-7-1 -0.113754 2660 18420 110 1831 1763 1000 194 196 29 100 100 0 1812 2047 1115 134 136 20 100 100 0 0.976 0.82 0.808 0.743 1.668 0.848 0.923 80 523 3315 3482 -0.036 1637 1678 1569 1913 0
Hs6-1-8-1 null 2850 18430 110 569 587 233 196 200 31 91 88 0 561 570 258 135 138 22 100 96 0 0.876 0.899 0.904 0.889 2.211 0.898 0.884 80 496 799 826 -0.192 373 426 391 435 0
Hs6-1-9-1 0.055544 3010 18430 100 2203 2528 1312 200 203 34 100 100 0 2470 2682 1491 137 141 25 100 100 0 0.859 0.915 0.918 0.953 1.421 0.898 0.945 80 456 4336 4873 -0.22 2003 2333 2328 2545 0
Hs6-1-10-1 null 3210 18430 110 483 450 184 201 204 37 83 82 0 382 414 193 137 141 24 87 87 0 1.151 0.899 1.084 1.099 1.717 0.919 0.753 80 518 527 526 0.203 282 245 249 277 0
Hs6-1-11-1 null 3370 18430 110 475 474 216 196 196 29 85 82 0 483 479 224 135 138 31 91 86 0 0.802 0.808 0.88 0.958 2.038 0.86 0.849 80 483 627 622 -0.319 279 348 278 344 0
Hs6-1-12-1 null 3540 18440 110 631 708 363 192 194 29 91 90 0 714 720 411 132 136 32 95 91 0 0.754 0.878 0.891 0.974 1.806 0.873 0.898 80 415 1021 1104 -0.407 439 582 516 588 0
Hs6-1-13-1 0.133817 3720 18430 180 1730 1601 418 189 192 30 99 98 0 1732 1626 411 135 137 21 99 99 0 0.965 0.947 0.958 0.942 1.342 0.955 0.965 256 1347 3138 2903 -0.051 1541 1597 1412 1491 0
Hs6-1-14-1 -0.105117 3890 18430 60 820 719 265 191 197 35 93 90 0 927 796 291 138 141 28 93 93 0 0.797 0.802 0.821 0.772 1.674 0.819 0.876 32 152 1418 1186 -0.327 629 789 528 658 0
Hs6-1-15-1 null 4070 18440 100 516 512 256 188 192 31 85 83 0 497 567 320 131 132 19 92 92 0 0.896 0.743 0.807 0.88 2.558 0.751 0.879 80 473 694 760 -0.158 328 366 324 436 0
Hs6-1-16-1 null 4250 18440 100 623 628 329 186 189 31 87 87 0 500 530 288 128 132 25 88 87 0 1.175 1.1 1.175 1.102 1.814 1.113 0.875 80 467 809 844 0.232 437 372 442 402 0
Hs6-1-17-1 -0.100953 4410 18420 90 1231 1176 663 184 186 31 92 90 0 1606 1345 799 133 135 21 90 90 0 0.711 0.818 0.811 0.878 2.25 0.834 0.938 52 384 2520 2204 -0.492 1047 1473 992 1212 0
Hs6-1-18-1 null 4590 18440 80 641 1007 2787 182 183 31 86 84 0 569 520 396 128 130 21 84 80 0 1.041 2.105 1.115 1.433 2.418 6.864 0.629 52 248 900 1217 0.058 459 441 825 392 0
Hs6-1-19-1 0.08317 4760 18440 180 2320 2201 547 191 194 34 98 98 0 2372 2263 555 138 141 28 99 99 0 0.953 0.946 0.936 0.92 1.377 0.944 0.964 256 1280 4363 4135 -0.069 2129 2234 2010 2125 0
Hs6-1-20-1 -0.319413 4930 18430 90 1034 954 440 192 196 38 100 96 0 1307 1229 599 132 136 27 100 96 0 0.717 0.695 0.699 0.698 1.566 0.7 0.919 52 315 2017 1859 -0.481 842 1175 762 1097 0

Total number of rows: 20000

Table truncated, full table size 3544 Kbytes.




Supplementary data files not provided
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