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Sample GSM50161 Query DataSets for GSM50161
Status Public on Jan 02, 2006
Title Cell Line_WTA10ng_onePCR
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell line treated with 1nm R1881 for 24 hours, 10ng 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, 10ng 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
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 2
% > 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 970 18350 100 312 319 138 132 137 46 82 72 0 647 617 304 195 198 50 85 83 0 0.398 0.443 0.383 0.332 2.481 0.4 0.639 80 505 632 609 -1.328 180 452 187 422 0
Hs6-1-2-1 -0.575432 1140 18350 100 446 456 208 128 133 46 90 82 0 804 715 394 180 185 45 82 80 0 0.51 0.613 0.524 0.608 1.82 0.553 0.818 80 432 942 863 -0.973 318 624 328 535 0
Hs6-1-3-1 null 1310 18350 70 160 168 62 126 132 42 46 28 0 566 477 232 183 185 43 71 71 0 0.089 0.143 0.229 0.189 4.202 0.112 0.126 32 236 417 336 -3.494 34 383 42 294 0
Hs6-1-4-1 null 1480 18350 100 283 282 121 126 132 43 77 66 0 572 493 263 185 188 43 76 71 0 0.406 0.506 0.463 0.402 2.604 0.451 0.709 80 486 544 464 -1.302 157 387 156 308 0
Hs6-1-5-1 null 1670 18350 100 185 207 90 125 130 43 55 41 0 334 428 270 179 183 44 71 63 0 0.387 0.329 0.325 0.338 2.689 0.288 0.518 80 437 215 331 -1.369 60 155 82 249 -50
Hs6-1-6-1 -0.243743 1830 18360 100 521 514 243 132 140 47 90 88 0 765 751 379 176 181 46 88 86 0 0.66 0.664 0.669 0.703 1.988 0.629 0.824 80 402 978 957 -0.598 389 589 382 575 0
Hs6-1-7-1 -0.144406 2000 18350 110 2322 2172 1416 138 153 73 97 92 0 2444 2243 1457 182 196 76 90 86 0 0.966 0.987 0.98 1.067 1.564 0.982 0.961 80 543 4446 4095 -0.051 2184 2262 2034 2061 0
Hs6-1-8-1 -0.416182 2190 18350 70 501 484 202 140 159 78 84 81 0 831 737 283 195 219 104 87 84 0 0.568 0.635 0.598 0.615 2.371 0.657 0.767 32 236 997 886 -0.817 361 636 344 542 0
Hs6-1-9-1 -0.08324 2350 18350 90 2334 2022 1204 131 140 54 96 94 0 2278 2074 1271 196 203 53 84 82 0 1.058 1.007 1.018 1.214 1.869 0.975 0.965 52 408 4285 3769 0.081 2203 2082 1891 1878 0
Hs6-1-10-1 null 2540 18350 90 382 370 161 130 139 56 84 78 0 609 544 269 193 202 76 76 73 0 0.606 0.684 0.674 0.819 2.337 0.599 0.687 52 407 668 591 -0.723 252 416 240 351 0
Hs6-1-11-1 null 2720 18360 70 378 403 143 134 142 64 93 87 0 694 619 199 188 211 96 93 93 0 0.482 0.624 0.594 0.524 1.968 0.571 0.675 32 236 750 700 -1.052 244 506 269 431 0
Hs6-1-12-1 -0.349194 2890 18360 70 446 437 194 134 152 76 81 81 0 766 680 290 183 204 95 84 84 0 0.535 0.61 0.601 0.546 1.608 0.549 0.695 32 200 895 800 -0.902 312 583 303 497 0
Hs6-1-13-1 -0.083288 3060 18350 190 674 689 260 135 144 60 95 92 0 883 857 261 190 208 79 93 92 0 0.778 0.831 0.809 0.798 1.487 0.855 0.824 256 1403 1232 1221 -0.363 539 693 554 667 0
Hs6-1-14-1 -0.189791 3230 18350 60 518 501 205 125 134 47 87 84 0 783 715 322 170 178 48 84 81 0 0.641 0.69 0.702 0.691 1.882 0.609 0.767 32 152 1006 921 -0.641 393 613 376 545 0
Hs6-1-15-1 -0.393499 3420 18350 70 566 529 198 142 148 56 90 84 0 837 749 315 190 198 67 87 84 0 0.655 0.692 0.624 0.517 2.427 0.637 0.83 32 236 1071 946 -0.61 424 647 387 559 0
Hs6-1-16-1 null 3590 18350 60 282 270 89 137 148 77 75 40 0 670 600 246 192 206 86 81 81 0 0.303 0.326 0.335 0.318 1.961 0.288 0.458 32 176 623 541 -1.721 145 478 133 408 0
Hs6-1-17-1 null 3750 18350 110 759 1294 2328 137 207 516 55 35 0 1123 1683 3288 185 271 627 53 45 0 0.663 0.772 0.762 0.794 1.804 0.796 0.947 80 554 1560 2655 -0.593 622 938 1157 1498 -100
Hs6-1-18-1 null 3940 18360 100 166 184 86 131 133 44 45 27 0 326 356 211 183 190 50 65 57 0 0.245 0.306 0.31 0.3 3.167 0.312 0.409 80 375 178 226 -2.031 35 143 53 173 -50
Hs6-1-19-1 0.022969 4110 18350 190 1269 1215 358 137 141 49 98 98 0 1313 1270 323 195 203 61 96 96 0 1.013 1.003 0.998 0.98 1.301 1.04 0.91 256 1204 2250 2153 0.018 1132 1118 1078 1075 0
Hs6-1-20-1 null 4290 18360 100 222 282 178 139 150 58 57 42 0 231 386 299 192 201 70 45 33 0 2.128 0.737 0.693 0.835 3.455 0.605 0.703 80 410 122 337 1.09 83 39 143 194 -50

Total number of rows: 20000

Table truncated, full table size 3498 Kbytes.




Supplementary data files not provided
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