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Sample GSM100155 Query DataSets for GSM100155
Status Public on Oct 12, 2006
Title N-56, NORM, M, GSF, 1 x ETOH, 24h
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 nGSF56, proliferating, 24h ETOH
Organism Homo sapiens
Characteristics nGSF56, proliferating, 24h ETOH
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16657.gif; format: GIF
Compound Based Treatment: 1 x ethanol
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
1 840 1361 451 235 389 1126 829 848 465 249 378 613 0 0 226 1363 127 118 88 98 73 84 1515 991 .345 2.895 1.622 2.109 1.612 2.743 52 282 5.339 .62 80 1700 9400 52 60 66 74 -100 1226 212 1014 2.607 764 552 .384 1.46 1.382 .546
2 1191 1912 458 212 733 1700 1165 1498 452 231 707 1286 0 0 517 1549 91 158 84 96 84 90 2433 1993 .431 2.319 1.819 1.911 1.52 2.101 32 128 3.549 .72 60 1840 9420 55 61 81 87 -100 1722 191 1531 2.089 1349 1158 .479 1.638 1.063 .712
3 3116 2873 474 205 2642 2668 3108 2673 468 216 2634 2468 0 0 863 963 98 126 100 100 100 100 5310 5102 .99 1.01 .937 1.017 .934 1.454 80 248 1.184 .92 100 1970 9400 51 61 92 102 0 2587 185 2403 .909 2407 2223 1.1 .844 -.137 -.245
4 605 548 479 200 126 348 478 234 477 203 -1 34 0 0 370 770 100 70 23 35 17 27 474 33 .362 2.762 null 1.049 .952 4.533 120 362 3.669 .73 120 2080 9400 50 62 102 114 -100 493 180 313 2.487 211 31 .402 null 1.315 null
5 2712 3711 466 194 2246 3517 2310 3196 470 199 1844 3002 0 0 2213 2385 101 60 100 100 100 100 5763 4846 .639 1.566 1.628 1.623 1.596 1.333 80 291 1.398 .93 110 2230 9400 50 61 117 128 0 3342 175 3167 1.41 2878 2703 .709 1.466 .496 .552
6 541 514 471 183 70 331 437 233 484 190 -34 50 0 0 274 763 153 67 20 45 15 33 401 16 .211 4.729 null .88 1.066 5.297 120 386 4.18 .63 120 2350 9400 50 62 129 141 -100 463 165 298 4.258 210 45 .235 null 2.09 null
7 2117 2033 459 178 1658 1855 2052 1775 461 188 1593 1597 0 0 462 914 91 65 100 100 100 100 3513 3190 .894 1.119 1.003 1.062 .983 1.508 80 322 1.437 .84 110 2510 9400 50 61 145 156 0 1831 160 1670 1.008 1598 1438 .993 .903 .011 -.148
8 2761 2427 449 177 2312 2250 2826 2284 460 190 2377 2107 0 0 447 754 92 63 100 100 100 100 4562 4484 1.028 .973 .886 .944 .913 1.318 80 278 1.124 .92 100 2640 9400 51 61 159 169 0 2186 159 2026 .876 2057 1897 1.141 .798 -.19 -.325
9 1725 1992 462 179 1263 1813 1860 1836 467 185 1398 1657 0 0 791 1091 97 55 90 100 88 100 3076 3055 .697 1.435 1.185 1.561 1.384 2.186 52 193 1.712 .82 80 2790 9400 52 60 175 183 0 1794 161 1633 1.293 1653 1492 .774 1.067 .37 .094
10 831 826 436 174 395 652 806 396 443 177 370 222 0 0 228 855 100 57 94 92 76 80 1047 592 .606 1.651 .6 .936 .717 2.627 52 177 3.7 .66 80 2910 9390 51 59 187 195 -100 744 157 587 1.486 357 200 .673 .54 .572 -.888
11 2411 703 446 168 1965 535 2579 389 456 178 2133 221 0 0 702 613 112 81 100 86 98 65 2500 2354 3.673 .272 .104 .156 .145 2.941 80 301 .69 .62 100 3040 9400 51 61 199 209 0 633 151 482 .245 350 199 4.079 .093 -2.028 -3.422
12 997 942 445 168 552 774 945 626 458 174 500 458 0 0 251 909 101 76 100 97 95 95 1326 958 .713 1.402 .916 1.089 .995 1.973 80 266 3.316 .63 100 3170 9400 51 61 212 222 -100 848 151 697 1.263 564 412 .792 .825 .337 -.278
13 1079 1006 455 170 624 836 1089 728 464 178 634 558 0 0 225 729 98 70 100 96 97 92 1460 1192 .746 1.34 .88 1.029 .985 2.063 80 238 2.447 .71 100 3310 9400 51 61 226 236 -100 906 153 753 1.206 656 502 .829 .793 .271 -.335
14 978 864 478 161 500 703 951 608 483 178 473 447 0 0 257 809 100 68 96 100 90 98 1203 920 .711 1.406 .945 1.204 1.124 1.865 80 285 2.937 .67 100 3440 9390 50 60 239 249 -100 778 145 633 1.266 548 403 .79 .851 .34 -.233
15 1260 1120 483 150 777 970 1259 991 490 162 776 841 0 0 257 523 96 55 100 100 100 100 1747 1617 .801 1.248 1.084 1.14 1.093 1.629 52 238 1.589 .84 90 3580 9400 51 60 253 262 0 1009 135 874 1.124 892 757 .89 .976 .169 -.035
16 2262 1861 496 139 1766 1722 2226 1805 520 151 1730 1666 0 0 333 479 149 67 100 100 100 100 3488 3396 1.026 .975 .963 .958 .918 1.356 52 260 1.021 .9 90 3700 9380 49 58 265 274 0 1676 125 1551 .878 1625 1500 1.139 .867 -.188 -.206
17 1414 1339 535 137 879 1202 1447 1201 559 150 912 1064 0 0 267 403 156 67 100 100 96 100 2081 1976 .731 1.367 1.167 1.388 1.334 1.464 52 278 1.56 .86 90 3840 9390 50 59 279 288 0 1206 123 1082 1.231 1082 958 .812 1.051 .3 .071
18 1026 476 551 136 475 340 1019 473 559 146 468 337 0 0 183 95 115 51 98 100 90 100 815 805 1.397 .716 .72 .747 .754 1.701 52 277 .897 .75 90 3990 9390 50 59 294 303 0 429 122 306 .645 426 303 1.551 .648 -.634 -.625
19 915 514 568 138 347 376 912 466 575 146 344 328 0 0 140 220 116 52 96 98 80 96 723 672 .923 1.084 .953 1.004 1.049 1.93 52 225 1.504 .68 90 4130 9400 51 60 308 317 0 463 124 339 .976 420 295 1.025 .859 -.035 -.22
20 2076 1727 589 152 1487 1575 2105 1764 598 156 1516 1612 0 0 518 538 111 46 98 100 97 100 3062 3128 .944 1.059 1.063 1.07 1.027 1.476 80 248 1.113 .94 100 4260 9390 50 60 321 331 0 1555 137 1418 .954 1589 1452 1.048 .958 -.068 -.063

Total number of rows: 44544

Table truncated, full table size 9952 Kbytes.




Supplementary data files not provided
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