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Sample GSM50134 Query DataSets for GSM50134
Status Public on Jan 02, 2006
Title Cell Line_WTA1ng_onePCR
Sample type RNA
 
Channel 1
Source name LnCAP_R, prostate cancer cell lines treated with 1nm synthetic androgen R1881 for 24 hours, 1ng RNA one WTA PCR, 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, 1ng RNA one WTA PCR, 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 Median of Ratios (635/532), 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 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 -0.860515 1430 18670 60 345 338 119 190 195 78 68 50 0 423 396 136 113 130 65 90 84 0 0.5 0.523 0.482 0.433 2.034 0.657 0.371 32 176 465 431 -1 155 310 148 283 0
Hs6-1-2-1 -0.463035 1610 18670 70 360 362 143 171 187 77 78 59 0 440 425 104 112 134 77 96 96 0 0.576 0.61 0.654 0.535 2.48 0.713 0.483 32 231 517 504 -0.795 189 328 191 313 0
Hs6-1-3-1 null 1780 18670 90 179 186 69 167 175 64 23 7 0 264 243 103 107 112 32 80 73 0 0.076 0.14 0.299 0.309 4.525 0.267 0.01 52 379 169 155 -3.71 12 157 19 136 -50
Hs6-1-4-1 null 1930 18660 80 239 246 81 164 171 69 51 25 0 325 280 115 105 110 32 78 75 0 0.341 0.469 0.564 0.566 2.535 0.527 0.173 52 318 295 257 -1.553 75 220 82 175 0
Hs6-1-5-1 null 2130 18670 50 265 271 71 170 175 60 75 33 0 344 346 50 113 130 64 100 100 0 0.411 0.433 0.384 0.363 2.827 0.469 0.224 12 104 326 334 -1.282 95 231 101 233 0
Hs6-1-6-1 -0.021175 2280 18680 100 396 402 168 158 166 59 83 73 0 398 379 178 104 107 26 91 86 0 0.81 0.887 0.895 0.936 2.382 0.903 0.672 80 456 532 519 -0.305 238 294 244 275 0
Hs6-1-7-1 -0.087823 2470 18680 110 1349 1348 656 161 171 63 95 93 0 1247 1197 556 109 113 33 97 93 0 1.044 1.091 1.107 1.102 1.714 1.146 0.908 80 534 2326 2275 0.062 1188 1138 1187 1088 0
Hs6-1-8-1 -0.259361 2650 18680 90 302 315 127 168 175 63 71 53 0 352 320 127 106 110 32 86 80 0 0.545 0.687 0.684 0.687 1.915 0.825 0.348 52 352 380 361 -0.876 134 246 147 214 0
Hs6-1-9-1 0.094678 2810 18680 100 957 983 513 173 175 62 92 90 0 770 797 426 105 109 28 93 91 0 1.179 1.171 1.188 1.164 2.078 1.19 0.9 80 458 1449 1502 0.237 784 665 810 692 0
Hs6-1-10-1 null 3000 18680 80 276 264 96 168 175 67 67 32 0 355 315 133 108 115 42 82 78 0 0.437 0.464 0.5 0.484 2.199 0.619 0.466 52 340 355 303 -1.193 108 247 96 207 0
Hs6-1-11-1 null 3180 18680 70 275 294 103 169 178 69 59 43 0 344 316 80 100 118 61 93 93 0 0.434 0.579 0.627 0.416 2.672 0.808 0.396 32 236 350 341 -1.203 106 244 125 216 0
Hs6-1-12-1 -0.721181 3350 18690 60 327 335 143 182 201 97 68 31 0 436 385 145 107 133 77 84 81 0 0.441 0.55 0.534 0.639 1.928 0.744 0.386 32 140 474 431 -1.182 145 329 153 278 0
Hs6-1-13-1 0.105823 3520 18690 200 439 446 154 170 197 436 15 0 0 405 376 122 112 137 395 6 0 0 0.918 1.045 0.993 0.986 2.128 1.099 0.946 316 1920 562 540 -0.123 269 293 276 264 0
Hs6-1-14-1 null 3700 18690 90 190 202 78 165 173 66 23 11 0 130 172 103 106 112 42 38 32 0 1.042 0.561 0.754 0.823 4.177 1.071 0.159 52 332 49 103 0.059 25 24 37 66 -50
Hs6-1-15-1 -0.580339 3880 18690 60 311 292 92 171 188 96 59 25 0 371 342 122 109 120 55 84 84 0 0.534 0.519 0.558 0.535 2.1 0.555 0.357 32 176 402 354 -0.904 140 262 121 233 0
Hs6-1-16-1 null 4040 18690 70 236 224 78 160 165 55 59 31 0 339 295 131 104 111 33 81 78 0 0.323 0.335 0.52 0.485 2.502 0.379 0.251 32 236 311 255 -1.629 76 235 64 191 0
Hs6-1-17-1 -0.149824 4220 18690 70 438 414 173 154 174 76 78 71 0 470 390 183 103 121 69 81 75 0 0.774 0.906 0.868 0.746 1.823 0.876 0.65 32 236 651 547 -0.37 284 367 260 287 0
Hs6-1-18-1 null 4400 18690 90 207 208 94 157 165 60 42 28 0 245 222 99 104 107 27 75 73 0 0.355 0.432 0.695 0.724 3.14 1.033 0.111 52 310 191 169 -1.496 50 141 51 118 -50
Hs6-1-19-1 -0.040838 4570 18690 180 517 516 161 163 171 64 94 91 0 480 457 108 108 115 36 96 95 0 0.952 1.011 0.961 0.938 1.732 1.112 0.714 256 1388 726 702 -0.072 354 372 353 349 0
Hs6-1-20-1 -0.176577 4750 18690 110 407 424 176 167 173 63 88 72 0 455 421 189 104 110 37 86 83 0 0.684 0.811 0.829 0.857 2.056 0.934 0.646 80 480 591 574 -0.548 240 351 257 317 0

Total number of rows: 20000

Table truncated, full table size 3417 Kbytes.




Supplementary data files not provided
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