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Sample GSM100158 Query DataSets for GSM100158
Status Public on Oct 12, 2006
Title N-40, NORM, M, GSF
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 nGSF40, 14 days DMEM F12, 12.9% FCS, G0
Organism Homo sapiens
Characteristics nGSF40, 14 days DMEM F12, 12.9% FCS, G0
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17595.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency
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
GSE4456 Androgen receptor coregulators
GSE6796 Fibroblasts from genital and extragenital regions of 46,XY individuals

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
1 300 200 122 61 178 139 290 199 125 63 168 138 0 0 84 81 31 18 97 95 91 87 317 306 1.281 .781 .821 .806 .835 1.737 80 383 1.097 .75 100 1880 9600 55 65 51 61 0 200 61 139 .782 199 138 1.278 .823 -.354 -.281
2 371 304 124 62 247 242 340 337 127 63 216 275 0 0 140 140 31 16 92 98 90 98 489 491 1.021 .98 1.273 .977 .853 2.248 52 154 1.224 .82 80 2040 9610 57 65 68 76 0 304 62 242 .981 338 275 1.019 1.275 -.027 .351
3 948 699 131 58 817 641 909 779 134 63 778 721 0 0 333 284 33 30 97 95 97 90 1458 1499 1.275 .785 .927 .694 .804 1.805 80 239 .913 .88 100 2150 9600 55 65 78 88 0 700 58 642 .786 780 722 1.272 .928 -.348 -.107
4 139 87 129 62 10 25 136 80 133 67 7 18 0 0 36 39 37 30 21 31 5 13 35 25 .4 2.5 2.571 .951 .882 4.098 80 226 2.002 .44 100 2280 9600 55 65 91 101 0 87 62 25 2.504 80 18 .399 2.576 1.324 1.365
5 645 1456 129 69 516 1387 648 1499 131 71 519 1430 0 0 144 260 30 22 100 100 100 100 1903 1949 .372 2.688 2.755 2.759 2.761 1.406 80 316 2.847 .91 100 2390 9590 54 64 102 112 0 1458 69 1389 2.692 1501 1432 .371 2.76 1.429 1.465
6 282 226 132 78 150 148 246 222 134 82 114 144 0 0 118 96 28 26 84 96 75 71 298 258 1.014 .987 1.263 .987 .93 2.873 32 110 1.357 .64 60 2560 9610 58 64 121 127 0 226 78 148 .988 222 144 1.012 1.265 -.017 .339
7 576 598 134 68 442 530 588 619 134 72 454 551 0 0 124 170 30 23 100 98 100 98 972 1005 .834 1.199 1.214 1.128 1.227 1.789 80 351 1.344 .89 110 2660 9580 52 63 128 139 0 599 68 531 1.201 620 552 .833 1.216 .264 .282
8 851 1239 138 65 713 1174 852 1223 138 67 714 1158 0 0 203 239 32 18 100 100 100 100 1887 1872 .607 1.647 1.622 1.69 1.67 1.313 80 285 1.728 .9 110 2800 9590 53 64 142 153 0 1241 65 1176 1.649 1225 1160 .606 1.624 .722 .7
9 636 398 140 66 496 332 636 406 142 67 496 340 0 0 179 138 33 17 100 100 100 100 828 836 1.494 .669 .685 .644 .694 1.651 80 284 .769 .88 100 2930 9590 54 64 156 166 0 399 66 333 .67 407 341 1.492 .687 -.577 -.542
10 196 96 138 70 58 26 189 91 141 71 51 21 0 0 44 27 37 18 62 53 34 31 84 72 2.231 .448 .412 .539 .5 3.553 32 126 3.498 .18 60 3070 9580 55 61 172 178 0 96 70 26 .449 91 21 2.227 .412 -1.155 -1.278
11 671 121 134 72 537 49 674 107 136 74 540 35 0 0 128 66 33 19 100 71 100 43 586 575 10.959 .091 .065 .072 .078 2.292 80 325 .385 .46 100 3200 9580 53 63 183 193 0 121 72 49 .091 107 35 10.941 .065 -3.452 -3.945
12 224 200 141 73 83 127 214 194 144 75 73 121 0 0 65 59 37 25 71 98 48 92 210 194 .654 1.53 1.658 1.495 1.601 3.214 52 228 2.159 .49 90 3330 9600 55 64 196 205 0 200 73 127 1.533 194 121 .652 1.66 .616 .731
13 295 193 143 67 152 126 297 193 147 71 154 126 0 0 60 54 36 25 100 97 87 90 278 280 1.206 .829 .818 .803 .788 1.769 80 287 1.05 .76 100 3480 9590 54 64 211 221 0 193 67 126 .83 193 126 1.204 .82 -.268 -.287
14 232 128 134 72 98 56 225 123 137 73 91 51 0 0 52 41 32 21 94 76 71 57 154 142 1.75 .571 .56 .475 .53 3.435 52 224 1.359 .44 90 3600 9590 54 63 223 232 0 128 72 56 .572 123 51 1.747 .561 -.805 -.833
15 242 149 132 79 110 70 226 144 134 80 94 65 0 0 74 46 30 23 94 92 76 65 180 159 1.571 .636 .691 .58 .575 2.576 52 221 1.097 .57 80 3740 9590 55 63 238 246 0 149 79 70 .637 144 65 1.569 .693 -.65 -.53
16 617 398 135 81 482 317 637 407 137 84 502 326 0 0 113 97 33 24 100 98 100 97 799 828 1.521 .658 .649 .606 .653 1.852 80 309 .766 .87 100 3880 9580 53 63 251 261 0 399 81 318 .659 408 327 1.518 .65 -.602 -.62
17 302 246 137 82 165 164 294 245 141 85 157 163 0 0 66 62 33 23 98 97 96 96 329 320 1.006 .994 1.038 1.001 .969 1.773 80 266 1.238 .76 100 4020 9580 53 63 265 275 0 246 82 164 .996 245 163 1.004 1.04 -.006 .056
18 234 339 137 83 97 256 233 340 142 86 96 257 0 0 55 51 34 24 85 100 65 100 353 353 .379 2.639 2.677 3.022 2.79 1.859 80 288 2.713 .7 110 4160 9590 53 64 278 289 0 340 83 256 2.643 341 257 .378 2.681 1.402 1.423
19 252 152 139 88 113 64 246 143 141 90 107 55 0 0 63 36 34 25 94 88 71 53 177 162 1.766 .566 .514 .579 .547 2.413 52 230 1.158 .54 90 4290 9580 53 62 292 301 0 152 88 64 .567 143 55 1.763 .515 -.818 -.958
20 697 673 140 92 557 581 706 690 144 94 566 598 0 0 153 131 35 24 100 100 100 100 1138 1164 .959 1.043 1.057 1.056 1.053 1.356 80 362 1.115 .91 110 4430 9580 52 63 305 316 0 674 92 582 1.045 691 599 .957 1.058 .063 .082

Total number of rows: 44544

Table truncated, full table size 9300 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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