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Sample GSM50166 Query DataSets for GSM50166
Status Public on Jan 02, 2006
Title Cell Line_WTA25ng_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 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, 25ng 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 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 2410 18910 100 691 675 228 216 233 195 86 62 0 1105 1025 363 243 268 387 80 60 0 0.551 0.587 0.603 0.592 1.555 0.567 0.76 80 484 1337 1241 -0.86 475 862 459 782 0
Hs6-1-2-1 -0.259171 2580 18920 100 1593 1581 607 211 229 206 96 90 0 2194 2099 891 219 242 410 93 85 0 0.7 0.729 0.724 0.749 1.408 0.752 0.775 80 430 3357 3250 -0.515 1382 1975 1370 1880 0
Hs6-1-3-1 null 2760 18930 90 355 396 136 200 213 77 78 50 0 744 696 210 213 216 53 92 92 0 0.292 0.406 0.371 0.345 3.362 0.376 0.4 52 363 686 679 -1.776 155 531 196 483 0
Hs6-1-4-1 null 2930 18930 100 553 548 186 207 218 78 92 82 0 920 861 308 223 233 61 95 90 0 0.496 0.534 0.544 0.507 2.081 0.539 0.724 80 484 1043 979 -1.01 346 697 341 638 0
Hs6-1-5-1 null 3110 18940 90 480 496 144 200 213 73 96 86 0 880 865 250 219 227 60 98 98 0 0.424 0.458 0.448 0.499 2.743 0.457 0.612 52 363 941 942 -1.239 280 661 296 646 0
Hs6-1-6-1 -0.153905 3280 18940 100 1696 1554 581 215 225 80 98 98 0 2141 1948 758 228 240 68 97 97 0 0.774 0.778 0.78 0.8 1.487 0.771 0.921 80 440 3394 3059 -0.369 1481 1913 1339 1720 0
Hs6-1-7-1 -0.154736 3450 18940 110 9638 8878 3973 228 249 135 100 100 0 9887 9300 4159 236 260 138 100 100 0 0.975 0.954 0.944 0.936 1.366 0.95 0.967 80 522 19061 17714 -0.036 9410 9651 8650 9064 0
Hs6-1-8-1 null 3640 18950 100 848 866 330 223 241 123 95 88 0 1203 1181 434 223 247 135 97 95 0 0.638 0.671 0.659 0.64 1.537 0.684 0.862 80 474 1605 1601 -0.649 625 980 643 958 0
Hs6-1-9-1 -0.121227 3820 18960 110 5433 5433 2734 217 227 81 100 100 0 6200 5871 3095 225 239 72 100 100 0 0.873 0.924 0.917 0.975 1.451 0.912 0.955 80 510 11191 10862 -0.196 5216 5975 5216 5646 0
Hs6-1-10-1 null 3990 18960 100 828 865 334 215 226 83 96 90 0 1256 1164 391 234 242 64 98 98 0 0.6 0.699 0.672 0.678 1.499 0.724 0.843 80 440 1635 1580 -0.737 613 1022 650 930 0
Hs6-1-11-1 null 4160 18970 100 699 678 232 213 221 77 96 91 0 957 938 356 231 241 64 95 92 0 0.669 0.658 0.679 0.67 1.542 0.653 0.792 80 459 1212 1172 -0.579 486 726 465 707 0
Hs6-1-12-1 -0.247109 4350 18980 80 1119 1064 368 212 217 75 96 92 0 1622 1441 549 222 237 79 96 94 0 0.648 0.699 0.687 0.722 1.761 0.683 0.823 52 291 2307 2071 -0.626 907 1400 852 1219 0
Hs6-1-13-1 -0.144598 4530 18980 170 2570 2456 612 239 253 96 100 99 0 3160 2938 730 251 273 103 99 98 0 0.801 0.825 0.829 0.842 1.321 0.832 0.926 208 1119 5240 4904 -0.32 2331 2909 2217 2687 0
Hs6-1-14-1 -0.11873 4690 18990 90 2066 2048 702 220 229 80 98 98 0 2485 2422 936 218 229 73 98 96 0 0.814 0.829 0.82 0.873 1.46 0.809 0.929 52 325 4113 4032 -0.296 1846 2267 1828 2204 0
Hs6-1-15-1 -0.484368 4880 18990 90 1028 994 361 218 229 83 96 96 0 1735 1533 570 234 243 69 98 98 0 0.54 0.597 0.583 0.602 1.474 0.594 0.863 52 364 2311 2075 -0.89 810 1501 776 1299 0
Hs6-1-16-1 null 5040 18990 100 448 458 147 223 228 80 81 71 0 837 791 283 229 240 67 95 88 0 0.37 0.418 0.398 0.395 2.492 0.415 0.596 80 440 833 797 -1.434 225 608 235 562 0
Hs6-1-17-1 -0.103812 5210 19000 100 2073 1957 889 224 237 101 98 96 0 2437 2319 1037 233 252 85 97 96 0 0.839 0.831 0.827 0.826 1.668 0.834 0.923 80 452 4053 3819 -0.253 1849 2204 1733 2086 0
Hs6-1-18-1 null 5380 19010 80 417 421 126 218 224 78 86 63 0 770 727 214 217 229 54 92 92 0 0.36 0.398 0.42 0.415 2.424 0.381 0.439 52 274 752 713 -1.475 199 553 203 510 0
Hs6-1-19-1 0.061423 5570 19010 180 4753 4358 1300 258 301 574 97 93 0 4742 4282 1340 274 315 169 98 97 0 1.006 1.023 1.018 1.047 1.411 1.014 0.956 256 1294 8963 8108 0.009 4495 4468 4100 4008 0
Hs6-1-20-1 -0.196878 5730 19020 100 2074 2058 915 216 230 89 100 98 0 2493 2573 1213 228 243 83 100 98 0 0.82 0.786 0.777 0.811 1.369 0.769 0.935 80 374 4123 4187 -0.286 1858 2265 1842 2345 0

Total number of rows: 20000

Table truncated, full table size 3619 Kbytes.




Supplementary data files not provided
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