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Sample GSM100135 Query DataSets for GSM100135
Status Public on Oct 12, 2006
Title N-AKPZF-I, NORM, M, PRF
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 AKPZF (prostate fibroblasts) 14 days DMEM F12, 12.9% FCS, Go
Organism Homo sapiens
Characteristics AKPZF (prostate fibroblasts) 14 days DMEM F12, 12.9% FCS, Go
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18022.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: prostate 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) [email protected]
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 GPL2938
Series (2)
GSE4453 Androgen receptor coregulators baseline comparisons
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
1 603 506 282 100 321 406 605 501 323 190 323 401 0 0 166 169 149 231 87 86 55 31 727 724 .791 1.265 1.241 1.296 1.218 1.839 80 391 1.538 .74 100 1350 9720 79 89 54 64 0 501 99 402 1.251 496 397 .799 1.228 .323 .296
2 465 1716 261 92 204 1624 420 1411 265 130 159 1319 0 0 198 1293 87 179 75 93 46 81 1828 1478 .126 7.961 8.296 6.129 6.711 2.259 32 116 8.02 .78 60 1480 9720 81 87 69 75 -100 1697 91 1606 7.875 1396 1305 .127 8.206 2.977 3.037
3 821 690 300 117 521 573 822 674 342 212 522 557 0 0 314 231 196 218 85 92 65 72 1094 1079 .909 1.1 1.067 1.226 1.06 2.033 80 371 1.212 .8 100 1620 9710 78 88 81 91 0 683 116 567 1.088 667 551 .919 1.056 .122 .078
4 440 1184 267 95 173 1089 431 860 275 120 164 765 0 0 146 842 78 110 65 96 53 90 1262 929 .159 6.295 4.665 4.948 5.339 3.049 32 137 10.482 .47 60 1780 9720 81 87 99 105 -100 1171 94 1077 6.227 851 757 .161 4.614 2.638 2.206
5 913 1782 323 144 590 1638 891 1772 466 662 568 1628 0 0 209 353 310 858 91 98 42 38 2228 2196 .36 2.776 2.866 2.903 2.77 1.449 80 324 2.777 .86 110 1900 9720 78 89 108 119 0 1763 142 1620 2.746 1753 1610 .364 2.835 1.457 1.503
6 421 2326 280 103 141 2223 417 1859 288 435 137 1756 0 0 153 1506 97 939 59 76 28 48 2364 1893 .063 15.766 12.818 12.846 12.297 2.658 52 150 19.275 .54 80 2040 9720 80 88 124 132 -100 2301 102 2199 15.596 1839 1737 .064 12.679 3.963 3.664
7 666 1386 345 253 321 1133 617 1341 456 1004 272 1088 0 0 309 711 364 4325 42 0 11 0 1454 1360 .283 3.53 4 3.832 2.603 2.842 120 328 4.636 .57 120 2170 9710 77 89 135 147 -100 1371 250 1121 3.491 1327 1076 .286 3.957 1.804 1.984
8 718 941 308 133 410 808 708 929 377 820 400 796 0 0 204 240 315 4967 63 0 13 0 1218 1196 .507 1.971 1.99 2.083 2.005 1.771 80 244 28.256 .54 110 2300 9720 78 89 148 159 0 931 132 799 1.949 919 787 .513 1.968 .963 .977
9 638 2844 271 92 367 2752 489 2477 274 99 218 2385 0 0 355 1775 83 41 76 100 55 100 3119 2603 .133 7.499 10.94 8.126 11.506 4.394 52 170 21.027 .29 80 2440 9710 79 87 164 172 -100 2813 91 2722 7.418 2450 2359 .135 10.822 2.891 3.436
10 424 359 276 99 148 260 409 331 284 103 133 232 0 0 125 132 82 43 76 98 37 93 408 365 .569 1.757 1.744 1.646 1.557 2.642 80 243 4.146 .34 100 2570 9710 78 88 176 186 -100 355 98 257 1.738 327 229 .575 1.726 .797 .787
11 791 1601 299 98 492 1503 791 799 301 108 492 701 0 0 337 1880 81 49 83 98 81 93 1995 1193 .327 3.055 1.425 1.5 .987 5.779 80 283 24.338 .19 110 2710 9720 78 89 189 200 -100 1584 97 1487 3.022 790 693 .331 1.409 1.595 .495
12 639 556 304 113 335 443 612 494 327 128 308 381 0 0 284 296 139 61 78 100 53 90 778 689 .756 1.322 1.237 1.097 1.107 2.39 32 107 1.61 .69 60 2820 9730 82 88 203 209 0 550 112 438 1.308 489 377 .764 1.224 .387 .291
13 1570 575 304 99 1266 476 568 536 317 108 264 437 0 0 5395 278 107 47 83 97 59 95 1742 701 2.66 .376 1.655 1.41 1.483 3.869 120 404 .438 .19 120 2980 9720 78 90 216 228 -100 569 98 471 .372 530 432 2.689 1.637 -1.427 .711
14 571 404 301 96 270 308 554 398 308 128 253 302 0 0 138 135 90 177 94 82 76 40 578 555 .877 1.141 1.194 1.179 1.203 1.795 52 207 1.464 .7 90 3120 9710 78 87 231 240 0 400 95 305 1.128 394 299 .886 1.181 .174 .24
15 1674 551 297 96 1377 455 591 600 335 167 294 504 0 0 5946 262 170 282 63 78 44 26 1832 798 3.026 .33 1.714 1.432 1.53 3.636 52 189 -2.444 -.05 80 3260 9690 77 85 246 254 -100 545 95 450 .327 594 499 3.059 1.696 -1.613 .762
16 791 704 307 102 484 602 777 688 825 140 470 586 0 0 201 203 3505 191 0 98 0 83 1086 1056 .804 1.244 1.247 1.288 1.216 1.744 80 307 1.582 .75 110 3390 9710 77 88 257 268 0 696 101 595 1.23 681 580 .813 1.233 .299 .303
17 695 543 297 107 398 436 663 512 311 146 366 405 0 0 217 195 120 123 87 96 78 87 834 771 .913 1.095 1.107 1.258 1.118 2.115 32 163 1.469 .69 70 3500 9710 79 86 270 277 0 537 106 431 1.084 506 401 .923 1.095 .116 .13
18 574 326 302 113 272 213 558 315 312 159 256 202 0 0 127 124 107 130 84 71 65 31 485 458 1.277 .783 .789 .714 .584 2.41 32 146 8.613 .14 60 3660 9710 80 86 287 293 0 322 112 211 .775 312 200 1.291 .781 -.368 -.357
19 497 634 294 101 203 533 491 637 311 119 197 536 0 0 126 138 139 87 66 100 18 100 736 733 .381 2.626 2.721 2.881 2.696 2.06 80 290 3.349 .57 100 3800 9720 79 89 299 309 0 627 100 527 2.597 630 530 .385 2.691 1.377 1.428
20 937 848 297 98 640 750 944 796 310 111 647 698 0 0 279 314 90 67 96 100 96 98 1390 1345 .853 1.172 1.079 1.171 1.182 1.771 52 188 1.325 .87 90 3940 9700 77 86 313 322 0 839 97 742 1.159 787 690 .863 1.067 .213 .094

Total number of rows: 44544

Table truncated, full table size 9667 Kbytes.




Supplementary data files not provided
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