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Sample GSM100154 Query DataSets for GSM100154
Status Public on Oct 12, 2006
Title N-56, NORM, M, GSF, 1 x 100nM DHT, 24h
Sample type RNA
 
Channel 1
Source name mixed reference (FR + CRG)
Organism Homo sapiens
Characteristics mixed reference (FR + CRG)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name nGSF56, proliferating, 24h 100nM DHT
Organism Homo sapiens
Characteristics nGSF56, proliferating, 24h 100nM DHT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16662.gif; format: GIF
Compound Based Treatment: 1 x 100nM DHT
Cell Line: foreskin fibroblast
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
1 805 1029 459 302 346 727 791 724 465 307 332 422 0 0 185 756 89 95 94 96 76 88 1073 754 .476 2.101 1.271 1.655 1.363 2.323 52 222 4.289 .62 80 1870 9320 76 84 59 67 -100 830 244 587 1.695 584 340 .59 1.026 .761 .036
2 606 611 457 320 149 291 485 373 466 327 28 53 0 0 342 580 89 98 35 37 25 27 440 81 .512 1.953 1.893 1.483 1.264 3.928 120 384 2.446 .64 120 1990 9320 74 86 69 81 -100 493 258 235 1.576 301 43 .635 1.527 .656 .611
3 3616 3507 453 313 3163 3194 3661 3517 463 317 3208 3204 0 0 904 867 92 94 100 100 100 100 6357 6412 .99 1.01 .999 1.014 1.009 1.292 80 240 1.046 .96 100 2140 9320 75 85 85 95 0 2829 253 2577 .815 2838 2585 1.227 .806 -.296 -.312
4 549 488 459 293 90 195 487 351 469 298 28 58 0 0 255 459 96 87 32 43 19 25 285 86 .462 2.167 2.071 1.397 1.276 3.984 120 382 3.215 .53 120 2260 9320 74 86 96 108 -100 394 236 157 1.748 283 47 .572 1.671 .806 .741
5 2520 3806 463 285 2057 3521 2576 3820 466 288 2113 3535 0 0 542 667 87 84 98 100 98 100 5578 5648 .584 1.712 1.673 1.763 1.668 1.317 80 286 1.72 .96 110 2400 9320 74 85 110 121 0 3071 230 2841 1.381 3082 2852 .724 1.35 .466 .433
6 500 436 449 269 51 167 450 332 450 275 1 63 0 0 202 345 85 77 26 46 15 24 218 64 .305 3.275 63 1.174 1.3 4.635 120 360 3.107 .51 120 2530 9320 74 86 123 135 -100 352 217 135 2.642 268 51 .379 50.828 1.402 5.668
7 2258 2490 452 270 1806 2220 2264 2404 454 278 1812 2134 0 0 705 640 84 77 100 100 98 100 4026 3946 .814 1.229 1.178 1.277 1.263 1.425 80 308 1.251 .93 110 2680 9320 74 85 138 149 -100 2009 218 1791 .992 1940 1722 1.008 .95 -.012 -.074
8 2580 2676 489 304 2091 2372 2532 2664 492 324 2043 2360 0 0 491 592 93 123 100 100 100 100 4463 4403 .882 1.134 1.155 1.125 1.147 1.316 80 312 1.206 .94 110 2820 9330 75 86 152 163 0 2159 245 1914 .915 2149 1904 1.093 .932 -.128 -.102
9 1749 1895 490 310 1259 1585 1775 1978 507 337 1285 1668 0 0 603 570 124 152 96 98 92 94 2844 2953 .794 1.259 1.298 1.347 1.278 1.679 52 222 1.294 .91 80 2960 9320 76 84 168 176 0 1529 250 1279 1.016 1596 1346 .985 1.047 .022 .067
10 786 741 481 299 305 442 748 587 485 297 267 288 0 0 188 464 102 86 93 71 65 59 747 555 .69 1.449 1.079 1.19 1.25 2.369 32 128 4.77 .58 60 3080 9340 79 85 181 187 -100 598 241 357 1.169 474 232 .855 .87 .226 -.2
11 2173 470 499 295 1674 175 2119 442 598 442 1620 147 0 0 317 173 1050 1248 98 0 5 0 1849 1767 9.566 .105 .091 .114 .117 2.016 52 337 .45 .47 90 3230 9330 76 85 194 203 0 379 238 141 .084 357 119 11.856 .073 -3.568 -3.772
12 733 695 483 279 250 416 733 507 487 289 250 228 0 0 141 506 105 97 87 78 62 56 666 478 .601 1.664 .912 1.05 1.096 3.526 32 186 3.402 .55 70 3370 9320 76 83 209 216 -100 561 225 336 1.343 409 184 .745 .736 .425 -.443
13 1003 918 477 281 526 637 987 890 510 340 510 609 0 0 168 252 376 494 80 71 9 7 1163 1119 .826 1.211 1.194 1.189 1.301 1.603 52 266 1.483 .8 90 3500 9330 76 85 221 230 0 741 227 514 .977 718 491 1.023 .963 -.033 -.054
14 859 716 485 301 374 415 854 654 516 375 369 353 0 0 176 336 371 484 47 21 2 7 789 722 .901 1.11 .957 1.019 .925 2.364 80 275 1.073 .81 100 3640 9330 76 86 235 245 0 578 243 335 .895 528 285 1.117 .772 -.16 -.374
15 838 809 471 299 367 510 848 781 484 319 377 482 0 0 189 229 101 98 88 98 80 94 877 859 .72 1.39 1.279 1.602 1.531 2.157 52 218 1.643 .74 90 3770 9330 76 85 248 257 0 653 241 411 1.121 630 389 .892 1.032 .165 .045
16 1587 1320 471 302 1116 1018 1595 1310 482 307 1124 1008 0 0 348 309 103 92 98 100 98 100 2134 2132 1.096 .912 .897 .926 .897 1.477 80 328 .984 .92 100 3910 9320 75 85 262 272 0 1065 244 821 .736 1057 813 1.359 .724 -.442 -.467
17 1093 1153 474 283 619 870 1079 1081 486 295 605 798 0 0 186 352 114 96 100 100 100 100 1489 1403 .711 1.405 1.319 1.381 1.273 1.494 52 265 1.83 .78 90 4050 9320 75 84 276 285 0 930 228 702 1.134 872 644 .882 1.064 .181 .09
18 768 679 461 280 307 399 756 567 482 283 295 287 0 0 133 389 197 93 76 98 28 76 706 582 .769 1.3 .973 1.161 .998 2.272 52 235 2.641 .46 90 4190 9320 75 84 290 299 0 548 226 322 1.049 457 232 .954 .785 .068 -.349
19 706 523 466 292 240 231 677 460 483 299 211 168 0 0 132 215 217 101 48 63 11 40 471 379 1.039 .963 .796 .844 .968 2.806 52 207 2.352 .41 80 4300 9330 77 85 302 310 0 422 236 186 .777 371 136 1.288 .642 -.365 -.638
20 1639 1570 464 291 1175 1279 1574 1496 465 299 1110 1205 0 0 445 301 119 97 100 100 96 100 2454 2315 .919 1.089 1.086 1.146 1.071 1.548 52 266 1.126 .89 90 4450 9320 75 84 316 325 0 1267 235 1032 .878 1207 972 1.139 .876 -.187 -.191

Total number of rows: 44544

Table truncated, full table size 9901 Kbytes.




Supplementary data files not provided
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