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Sample GSM50164 Query DataSets for GSM50164
Status Public on Jan 02, 2006
Title Cell Line_WTA25ng_15mindeg_twoPCR
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell line treated with 1nm R1881 for 24 hours, 25ng 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, 25ng total RNA WTA two PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See the MIAME checklist
15 minutes RNA degradation
 
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 -0.904046 2390 18900 80 390 369 143 158 162 55 82 73 0 932 822 358 240 248 72 84 82 0 0.335 0.363 0.348 0.338 2.348 0.325 0.603 52 321 1322 1191 -1.578 390 932 369 822 0
Hs6-1-2-1 -0.463561 2550 18900 90 994 857 357 154 167 181 90 76 0 1602 1314 658 235 242 69 90 88 0 0.614 0.652 0.657 0.735 2.25 0.656 0.613 52 374 2596 2171 -0.704 994 1602 857 1314 0
Hs6-1-3-1 null 2740 18910 60 246 265 98 147 152 54 81 46 0 718 642 286 223 235 77 81 78 0 0.2 0.282 0.274 0.279 2.798 0.223 0.359 32 176 964 907 -2.322 246 718 265 642 0
Hs6-1-4-1 -1.041903 2920 18910 60 396 378 146 165 178 70 78 71 0 900 828 326 242 278 134 84 84 0 0.351 0.363 0.312 0.273 2.777 0.315 0.525 32 176 1296 1206 -1.51 396 900 378 828 0
Hs6-1-5-1 null 3100 18920 100 230 247 107 159 172 109 40 11 0 436 535 333 248 266 89 58 51 0 0.378 0.307 0.312 0.358 2.859 0.268 0.472 80 473 666 782 -1.404 230 436 247 535 -50
Hs6-1-6-1 -0.204335 3260 18920 90 1031 971 429 158 167 61 94 92 0 1476 1280 542 235 241 65 92 88 0 0.703 0.778 0.778 0.738 1.6 0.756 0.827 52 343 2507 2251 -0.508 1031 1476 971 1280 0
Hs6-1-7-1 0.051397 3440 18920 120 4034 4958 3575 166 179 72 99 99 0 3875 4423 3040 255 273 115 98 95 0 1.069 1.15 1.15 1.167 1.711 1.165 0.933 120 649 7909 9381 0.096 4034 3875 4958 4423 0
Hs6-1-8-1 -0.2577 3630 18920 70 720 655 292 163 185 88 84 81 0 1043 1012 375 257 290 153 90 87 0 0.709 0.652 0.655 0.569 1.969 0.601 0.689 32 224 1763 1667 -0.496 720 1043 655 1012 0
Hs6-1-9-1 0.058861 3780 18930 100 3517 3639 2235 169 178 68 100 98 0 2981 3309 1991 256 272 85 95 93 0 1.229 1.137 1.127 1.085 1.717 1.131 0.921 80 465 6498 6948 0.297 3517 2981 3639 3309 0
Hs6-1-10-1 null 3980 18930 100 411 433 234 165 173 63 75 61 0 642 655 393 257 270 80 73 62 0 0.639 0.673 0.613 0.613 1.812 0.592 0.772 80 466 1053 1088 -0.646 411 642 433 655 -50
Hs6-1-11-1 -0.347644 4120 18930 60 489 468 162 179 189 75 87 78 0 887 808 328 267 296 132 81 78 0 0.5 0.534 0.526 0.492 1.618 0.477 0.729 32 164 1376 1276 -1 489 887 468 808 0
Hs6-1-12-1 -0.435388 4320 18930 70 800 713 316 165 208 129 84 78 0 1268 1092 439 249 296 159 84 84 0 0.623 0.65 0.621 0.565 1.522 0.599 0.749 32 212 2068 1805 -0.683 800 1268 713 1092 0
Hs6-1-13-1 0.030669 4510 18940 200 1616 1526 524 175 190 91 97 95 0 1781 1644 500 286 309 129 95 92 0 0.964 0.995 0.994 0.991 1.692 0.989 0.919 316 1725 3397 3170 -0.053 1616 1781 1526 1644 0
Hs6-1-14-1 null 4680 18950 100 158 173 75 164 169 56 13 8 0 230 234 88 251 257 71 11 6 0 0.286 -0.529 0.676 0.536 3.802 0.502 0.077 80 337 388 407 -1.806 158 230 173 234 -50
Hs6-1-15-1 -0.19651 4840 18950 80 562 536 289 157 164 59 76 71 0 933 837 453 236 245 72 76 75 0 0.581 0.631 0.618 0.478 3.144 0.585 0.727 52 304 1495 1373 -0.783 562 933 536 837 0
Hs6-1-16-1 null 5030 18950 60 347 348 119 163 177 68 78 65 0 1001 935 304 248 312 202 90 78 0 0.244 0.269 0.247 0.24 1.805 0.24 0.594 32 176 1348 1283 -2.035 347 1001 348 935 0
Hs6-1-17-1 -0.109858 5180 18950 90 1902 1646 777 156 161 53 92 92 0 1953 1775 926 245 252 70 90 88 0 1.022 0.974 0.926 1.059 1.935 0.913 0.899 52 400 3855 3421 0.031 1902 1953 1646 1775 0
Hs6-1-18-1 null 5380 18960 100 243 255 97 157 163 52 56 43 0 410 511 301 248 257 72 60 51 0 0.531 0.373 0.309 0.308 3.345 0.247 0.429 80 373 653 766 -0.913 243 410 255 511 -50
Hs6-1-19-1 0.220817 5540 18960 190 3560 3307 920 182 197 80 98 98 0 2982 2754 753 291 318 125 96 95 0 1.255 1.269 1.262 1.308 1.386 1.248 0.957 256 1448 6542 6061 0.328 3560 2982 3307 2754 0
Hs6-1-20-1 null 5730 18970 100 215 240 134 174 191 83 30 13 0 283 309 172 259 277 91 27 8 0 1.708 1.32 0.893 1.094 3.894 0.888 0.367 80 394 498 549 0.772 215 283 240 309 -50

Total number of rows: 20000

Table truncated, full table size 3532 Kbytes.




Supplementary data files not provided
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