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Sample GSM100137 Query DataSets for GSM100137
Status Public on Oct 12, 2006
Title LNCaP, 24h 100nM DHT/MR
Sample type RNA
 
Channel 1
Source name mixed reference (CRG+ FR)
Organism Homo sapiens
Characteristics mixed reference (CRG+ FR)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name LNCaP, 24h 100nM DHT
Organism Homo sapiens
Characteristics LNCaP, 24h 100nM DHT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16990.gif; format: GIF
Compound Based Treatment: 100nM DHT
Cell Line: LNCaP
Culture Synchrony: proliferation
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Mar 13, 2006
Last update date Oct 12, 2006
Contact name Paul-Martin Holterhus
E-mail(s) holterhus@pediatrics.uni-kiel.de
Phone +49 (0) 431-597 3959
Fax +49 (0) 431-597 3966
Organization name Universitätsklinikum Schleswig-Holstein
Department Pädiatrische Endokrinologie und Diabetologie
Lab Klinik für Allgemeine Pädiatrie
Street address Campus Kiel, Schwanenweg 20
City Kiel
ZIP/Postal code D-24105
Country Germany
 
Platform ID GPL3039
Series (3)
GSE4453 Androgen receptor coregulators baseline comparisons
GSE4454 Androgen receptor-coregulators hormone responsiveness LNCaP / GSF
GSE4456 Androgen receptor coregulators

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 491 210 338 115 153 95 468 193 345 124 130 78 0 0 100 82 83 52 75 65 43 40 248 208 1.611 .621 .6 .566 .555 3.898 32 192 1.412 .46 70 1600 9530 53 60 52 59 0 202 110 91 .596 185 75 1.677 .576 -.746 -.796
2 716 582 328 106 388 476 635 635 326 113 307 529 0 0 362 358 77 43 78 81 68 75 864 836 .815 1.227 1.723 1.163 1.303 2.006 32 128 1.216 .87 60 1740 9520 53 59 67 73 0 559 102 457 1.178 610 508 .849 1.654 .236 .726
3 1675 1477 337 111 1338 1366 1749 1573 338 113 1412 1462 0 0 418 434 73 42 98 100 97 98 2704 2874 .98 1.021 1.035 1.029 1.034 1.664 80 339 1.072 .95 100 1860 9500 49 59 77 87 0 1418 107 1311 .98 1510 1404 1.02 .994 -.029 -.009
4 431 256 341 111 90 145 416 196 349 114 75 85 0 0 168 165 76 40 50 68 31 50 235 160 .621 1.611 1.133 .906 .946 4.051 32 125 1.974 .48 60 2010 9520 53 59 94 100 0 246 107 139 1.547 188 82 .646 1.088 .629 .122
5 1210 704 332 127 878 577 1215 702 335 134 883 575 0 0 294 186 70 47 100 100 98 98 1455 1458 1.522 .657 .651 .659 .66 1.553 80 378 .727 .88 100 2130 9500 49 59 104 114 0 676 122 554 .631 674 552 1.585 .625 -.664 -.678
6 535 403 337 133 198 270 511 243 339 138 174 110 0 0 209 376 70 48 65 56 56 53 468 284 .733 1.364 .632 .67 .702 3.89 32 124 2.416 .63 60 2280 9520 53 59 121 127 0 387 128 259 1.309 233 106 .764 .607 .389 -.72
7 1051 655 335 108 716 547 1063 648 340 115 728 540 0 0 227 183 64 43 98 100 98 98 1263 1268 1.309 .764 .742 .769 .759 1.588 80 305 .846 .9 100 2400 9510 50 60 131 141 0 629 104 525 .733 622 518 1.363 .712 -.447 -.49
8 1756 508 334 96 1422 412 1756 503 340 103 1422 407 0 0 362 138 68 41 100 100 100 100 1834 1829 3.451 .29 .286 .28 .273 1.48 80 309 .337 .89 100 2540 9510 50 60 145 155 0 488 92 396 .278 483 391 3.595 .275 -1.846 -1.864
9 1004 786 325 93 679 693 935 689 328 99 610 596 0 0 312 352 69 39 100 100 100 100 1372 1206 .98 1.021 .977 1.019 1.042 1.542 32 106 1.082 .87 60 2680 9530 54 60 161 167 0 755 89 665 .98 661 572 1.021 .938 -.029 -.092
10 370 132 331 101 39 31 354 129 333 106 23 28 0 0 101 52 73 37 28 45 12 20 70 51 1.258 .795 1.217 .792 .755 4.289 120 394 4.893 .11 120 2800 9510 49 61 170 182 0 127 97 30 .763 124 27 1.31 1.169 -.39 .225
11 1552 708 325 99 1227 609 1552 689 327 103 1227 590 0 0 286 166 74 38 100 100 100 100 1836 1817 2.015 .496 .481 .493 .491 1.392 80 277 .542 .91 100 2940 9510 50 60 185 195 0 680 95 585 .477 661 566 2.099 .462 -1.069 -1.115
12 479 216 321 100 158 116 467 196 328 109 146 96 0 0 136 93 69 50 71 71 53 46 274 242 1.362 .734 .658 .717 .964 3.361 32 166 1.51 .5 70 3070 9520 52 59 199 206 0 207 96 111 .705 188 92 1.419 .631 -.505 -.664
13 646 351 335 94 311 257 649 343 356 110 314 249 0 0 119 105 136 55 92 98 62 93 568 563 1.21 .826 .793 .821 .77 1.853 80 290 1.073 .74 100 3220 9510 50 60 213 223 0 337 90 247 .793 329 239 1.26 .761 -.334 -.393
14 642 439 374 104 268 335 627 435 400 115 253 331 0 0 121 129 148 56 87 97 35 96 603 584 .8 1.25 1.308 1.276 1.247 1.666 80 256 1.541 .67 110 3340 9510 49 60 224 235 0 421 100 322 1.2 418 318 .833 1.256 .263 .329
15 385 110 379 102 6 8 371 105 384 108 -8 3 0 0 82 44 85 41 16 16 3 5 14 -5 .75 1.333 null .478 .43 4.401 120 314 2.589 .19 120 3480 9510 49 61 238 250 0 106 98 8 1.28 101 3 .781 null .356 null
16 340 114 353 104 -13 10 341 105 357 107 -12 1 0 0 66 52 78 37 10 23 0 6 -3 -11 null null null .7 .556 5.141 120 306 -1 -1 120 3610 9510 49 61 251 263 0 109 100 10 null 101 1 null null null null
17 362 133 344 107 18 26 342 116 346 110 -2 9 0 0 91 68 72 40 21 28 10 15 44 7 .692 1.444 null .665 .704 3.926 120 348 2.618 .26 120 3750 9510 49 61 265 277 0 128 103 25 1.387 111 9 .721 null .472 null
18 539 189 334 111 205 78 533 183 343 112 199 72 0 0 92 62 71 39 98 67 75 46 283 271 2.628 .38 .362 .367 .379 2.333 52 191 1.263 .39 90 3880 9510 50 59 279 288 0 181 107 75 .365 176 69 2.737 .347 -1.453 -1.525
19 475 149 355 112 120 37 465 134 358 114 110 22 0 0 126 98 73 40 65 36 38 12 157 132 3.243 .308 .2 .326 .305 3.47 120 351 1.611 .39 120 4020 9510 49 61 292 304 0 143 108 36 .296 129 21 3.378 .192 -1.756 -2.381
20 1802 4422 379 115 1423 4307 1773 4304 379 121 1394 4189 0 0 367 1224 77 47 100 100 100 100 5730 5583 .33 3.027 3.005 2.985 2.912 1.361 80 220 3.234 .93 100 4160 9510 50 60 307 317 0 4245 110 4135 2.906 4132 4022 .344 2.885 1.539 1.529

Total number of rows: 44544

Table truncated, full table size 9518 Kbytes.




Supplementary data files not provided
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