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Sample GSM100138 Query DataSets for GSM100138
Status Public on Oct 12, 2006
Title N-33, NORM, M, GSF, 6 x ETOH, 14d
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 nGSF33, G0, 6 x ETOH, 14 days
Organism Homo sapiens
Characteristics nGSF33, G0, 6 x ETOH, 14 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15601.gif; format: GIF
Compound Based Treatment: 6 x ethanol
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
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
1 596 509 231 148 365 361 623 490 235 151 392 342 0 0 139 229 55 57 98 88 94 84 726 734 1.011 .989 .872 .958 .976 2.098 52 305 1.608 .74 90 1790 9130 48 57 30 39 0 467 136 331 .908 450 314 1.102 .801 -.14 -.321
2 677 648 214 119 463 529 735 692 220 126 521 573 0 0 323 333 54 51 84 96 78 84 992 1094 .875 1.143 1.1 1.209 1.046 4.03 32 100 1.876 .57 60 1930 9160 53 59 46 52 0 595 109 485 1.049 635 526 .954 1.009 .068 .013
3 1629 1563 234 131 1395 1432 1606 1572 238 138 1372 1441 0 0 382 370 56 53 100 100 100 100 2827 2813 .974 1.027 1.05 1.023 1.06 1.47 80 331 1.148 .88 110 2050 9130 47 58 55 66 0 1434 120 1314 .942 1443 1322 1.061 .964 -.086 -.053
4 514 450 228 137 286 313 426 429 229 144 198 292 0 0 260 288 50 52 81 78 71 75 599 490 .914 1.094 1.475 1.099 .888 3.841 32 100 1.941 .56 60 2170 9140 51 57 70 76 0 413 126 287 1.004 394 268 .996 1.353 .006 .437
5 1132 2575 233 128 899 2447 1143 2578 238 137 910 2450 0 0 322 499 54 65 98 100 93 100 3346 3360 .367 2.722 2.692 2.962 2.66 1.773 80 373 2.791 .87 110 2310 9120 46 57 81 92 0 2363 117 2246 2.498 2366 2248 .4 2.471 1.321 1.305
6 526 447 227 110 299 337 498 495 228 116 271 385 0 0 246 282 47 51 71 71 68 65 636 656 .887 1.127 1.421 .97 1.165 3.516 32 115 1.511 .75 60 2450 9130 50 56 98 104 0 410 101 309 1.034 454 353 .967 1.304 .049 .383
7 1117 1636 227 121 890 1515 1119 1574 233 133 892 1453 0 0 349 497 52 57 100 100 100 100 2405 2345 .587 1.702 1.629 1.739 1.766 1.629 80 279 1.816 .89 100 2580 9120 47 57 109 119 0 1501 111 1390 1.562 1445 1333 .64 1.495 .644 .58
8 1249 1298 242 135 1007 1163 1259 1291 243 144 1017 1156 0 0 267 309 57 65 100 100 100 100 2170 2173 .866 1.155 1.137 1.156 1.137 1.449 80 346 1.268 .89 110 2710 9120 46 57 121 132 0 1191 124 1067 1.06 1185 1061 .943 1.043 .084 .061
9 1091 752 256 131 835 621 1098 723 259 137 842 592 0 0 374 258 62 59 96 96 96 96 1456 1434 1.345 .744 .703 .771 .701 2.511 32 173 .979 .77 70 2870 9120 48 55 139 146 0 690 120 570 .683 664 543 1.465 .645 -.551 -.632
10 511 415 247 137 264 278 490 392 250 140 243 255 0 0 122 159 60 53 98 97 87 90 542 498 .95 1.053 1.049 1.01 1.116 2.099 80 274 1.877 .62 100 2990 9110 46 56 150 160 0 381 126 255 .966 360 234 1.035 .963 -.049 -.054
11 1184 251 236 128 948 123 1220 245 239 133 984 117 0 0 254 91 55 57 100 76 100 51 1071 1101 7.707 .13 .119 .118 .127 2.338 80 266 .353 .56 110 3120 9120 46 57 162 173 0 230 117 113 .119 225 107 8.398 .109 -3.07 -3.196
12 953 1016 236 128 717 888 952 980 243 134 716 852 0 0 275 301 50 54 97 100 97 100 1605 1568 .807 1.238 1.19 1.339 1.298 1.844 80 289 1.367 .87 110 3260 9120 46 57 176 187 0 932 117 815 1.137 899 782 .88 1.092 .185 .127
13 526 398 245 146 281 252 523 398 248 146 278 252 0 0 88 101 55 53 100 98 98 92 533 530 1.115 .897 .906 .866 .88 1.751 52 235 1.463 .63 90 3390 9110 46 55 190 199 0 365 134 231 .823 365 231 1.215 .832 -.281 -.265
14 761 683 258 140 503 543 753 700 265 142 495 560 0 0 158 184 57 53 100 100 100 98 1046 1055 .926 1.08 1.131 1.056 1.099 1.581 80 280 1.322 .82 100 3530 9110 46 56 204 214 0 627 128 498 .991 642 514 1.009 1.038 -.013 .054
15 1042 913 266 145 776 768 1016 930 277 155 750 785 0 0 198 337 73 80 100 96 100 92 1544 1535 1.01 .99 1.047 .95 1.08 1.676 52 232 1.265 .86 90 3650 9110 46 55 216 225 0 838 133 705 .908 854 720 1.101 .961 -.139 -.058
16 1036 596 258 142 778 454 1047 610 271 158 789 468 0 0 147 160 81 87 100 98 100 94 1232 1257 1.714 .584 .593 .546 .589 1.55 52 264 .788 .83 90 3790 9100 45 54 230 239 0 547 130 417 .536 560 430 1.867 .544 -.901 -.877
17 729 647 274 138 455 509 749 633 283 149 475 495 0 0 146 173 71 71 100 100 96 98 964 970 .894 1.119 1.042 1.128 1.139 1.603 80 278 1.377 .84 100 3940 9110 46 56 245 255 0 594 127 467 1.027 581 454 .974 .956 .038 -.064
18 458 423 267 138 191 285 449 412 273 146 182 274 0 0 96 123 60 63 95 97 77 87 476 456 .67 1.492 1.505 1.573 1.527 2.201 80 280 2.207 .64 100 4070 9110 46 56 258 268 0 388 127 262 1.369 378 251 .73 1.382 .454 .466
19 471 311 277 143 194 168 477 303 279 149 200 160 0 0 86 92 58 64 94 88 82 61 362 360 1.155 .866 .8 .879 .763 2.244 52 271 1.821 .56 90 4220 9100 45 54 273 282 0 285 131 154 .795 278 147 1.258 .734 -.331 -.446
20 1018 938 290 143 728 795 1051 1021 291 151 761 878 0 0 218 337 60 64 100 97 100 93 1523 1639 .916 1.092 1.154 1.025 1.088 1.921 80 256 1.385 .84 100 4360 9110 46 56 287 297 0 861 131 730 1.002 937 806 .998 1.059 .003 .082

Total number of rows: 44544

Table truncated, full table size 9609 Kbytes.




Supplementary data files not provided
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