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Sample GSM93629 Query DataSets for GSM93629
Status Public on Jan 25, 2006
Title Prostate - LNCaP
Sample type RNA
 
Channel 1
Source name LNCaP control
Organism Homo sapiens
Characteristics LNCaP control
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name LNCaP 1uM 5-aza-dC 5 days
Organism Homo sapiens
Characteristics LNCaP 1uM 5-aza-dC 5 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27543.gif
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 Jan 24, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3295
Series (1)
GSE4089 DNA methyltransferase inhibitor 5-aza-dC-treated prostate cancer cell lines

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 907 895 177 171 730 724 962 969 185 191 785 798 0 0 297 351 49 85 100 93 100 90 1454 1583 1.008 .992 1.017 .859 .986 2.714 32 226 1.032 .81 70 1850 8140 18 25 13 20 0 1091 209 883 1.209 1182 973 .827 1.24 .274 .31 .31
2 654 396 181 186 473 210 685 394 193 199 504 208 0 0 207 157 57 80 100 75 90 65 683 712 2.252 .444 .413 .446 .471 2.719 32 222 .435 .57 70 1990 8130 17 24 27 34 0 483 227 256 .541 480 254 1.847 .503 -.885 -.991 -.991
3 1020 1087 186 195 834 892 941 1089 232 232 755 894 0 0 660 743 177 205 78 68 68 65 1726 1649 .935 1.07 1.184 .955 1.069 2.036 32 166 1.091 .83 60 2120 8130 18 24 41 47 0 1326 238 1088 1.304 1328 1090 .767 1.444 .383 .53 .53
4 20610 22561 200 185 20410 22376 19065 23011 212 198 18865 22826 0 0 15204 14910 90 93 96 100 94 94 42786 41691 .912 1.096 1.21 1.175 1.076 1.984 52 315 1.053 .86 80 2280 8140 18 26 56 64 0 27513 226 27288 1.337 28062 27837 .748 1.476 .419 .561 .561
5 696 772 200 181 496 591 727 680 210 195 527 499 0 0 223 339 71 85 96 96 93 93 1087 1026 .839 1.192 .947 1.059 1.098 1.961 32 212 .228 .27 70 2430 8150 19 26 71 78 0 941 221 721 1.453 829 609 .688 1.155 .539 .208 .208
6 360 385 192 181 168 204 271 292 198 188 79 111 0 0 219 253 54 75 57 53 42 40 372 190 .824 1.214 1.405 1.22 1.207 3.253 52 292 1.318 .72 80 2570 8130 17 25 85 93 -50 470 221 249 1.481 356 135 .675 1.713 .566 .777
7 626 637 197 188 429 449 585 608 202 197 388 420 0 0 239 169 53 84 96 100 96 93 878 808 .955 1.047 1.082 1.231 1.156 2.588 32 216 .995 .71 70 2710 8150 19 26 99 106 0 777 229 548 1.276 741 512 .783 1.32 .352 .401 .401
8 24962 27692 192 185 24770 27507 27151 29166 201 199 26959 28981 0 0 11215 11090 58 86 100 100 100 100 52277 55940 .9 1.11 1.075 1.241 1.156 2.307 52 364 1.091 .88 90 2860 8140 17 26 113 122 0 33771 226 33545 1.354 35568 35343 .738 1.311 .438 .391 .391
9 977 1272 202 189 775 1083 969 1224 204 200 767 1035 0 0 546 665 54 89 87 100 87 93 1858 1802 .716 1.397 1.349 1.527 1.397 2.811 32 227 1.383 .78 70 3010 8150 19 26 129 136 0 1551 230 1321 1.704 1493 1262 .587 1.646 .769 .719 .719
10 653 653 207 174 446 479 676 587 201 185 469 413 0 0 95 195 43 88 100 100 100 100 925 882 .931 1.074 .881 1.031 .947 1.57 12 104 1.103 .77 50 3150 8140 19 24 144 149 0 796 212 584 1.31 716 504 .764 1.074 .389 .103 .103
11 4012 4372 190 184 3822 4188 2963 2969 196 194 2773 2785 0 0 2877 3101 68 81 98 100 97 100 8010 5558 .913 1.096 1.004 1.189 1.008 2.963 80 447 1.093 .83 100 3300 8140 17 27 157 167 0 5332 224 5107 1.336 3621 3396 .748 1.225 .418 .293 .293
12 4366 3831 190 199 4176 3632 4499 3995 196 201 4309 3796 0 0 1824 1952 55 78 100 93 100 93 7808 8105 1.15 .87 .881 .815 .93 1.915 32 218 .913 .88 70 3460 8140 18 25 174 181 0 4672 243 4429 1.061 4872 4629 .943 1.074 .085 .103 .103
13 2193 1919 192 188 2001 1731 1957 1841 201 197 1765 1653 0 0 1122 1120 60 81 98 92 96 86 3732 3418 1.156 .865 .937 .924 .947 2.504 52 286 .905 .86 80 3600 8140 18 26 188 196 0 2340 229 2111 1.055 2245 2016 .948 1.142 .077 .192 .192
14 928 794 195 174 733 620 972 847 199 191 777 673 0 0 345 410 53 76 100 90 93 81 1353 1450 1.182 .846 .866 .868 .939 2.32 32 164 .882 .69 60 3750 8140 19 25 204 210 0 968 212 756 1.032 1033 821 .969 1.056 .045 .079 .079
15 17682 18929 192 183 17490 18746 19368 21595 201 193 19176 21412 0 0 11677 13453 58 75 93 97 93 93 36236 40588 .933 1.072 1.117 .956 1.138 3.504 80 423 1.114 .9 100 3890 8140 17 27 216 226 0 23084 223 22861 1.307 26335 26112 .765 1.362 .386 .445 .445
16 9361 9636 192 180 9169 9456 10311 10677 196 188 10119 10497 0 0 3301 4128 52 76 100 98 100 96 18625 20616 .97 1.031 1.037 .925 1.088 2.4 52 278 1.076 .91 80 4040 8140 18 26 232 240 0 11751 220 11532 1.258 13021 12801 .795 1.265 .331 .339 .339
17 867 533 189 174 678 359 926 501 196 184 737 327 0 0 284 267 51 75 100 87 100 84 1037 1064 1.889 .529 .444 .566 .558 2.066 32 219 .529 .58 70 4180 8140 18 25 246 253 0 650 212 438 .646 611 399 1.549 .541 -.631 -.886 -.886
18 591 429 202 191 389 238 583 412 208 200 381 221 0 0 154 185 55 76 96 81 96 68 627 602 1.634 .612 .58 .532 .637 2.276 32 164 1.133 .52 60 4330 8140 19 25 262 268 0 523 233 290 .746 502 270 1.34 .707 -.423 -.499 -.499
19 5656 4866 207 189 5449 4677 6068 5206 215 198 5861 5017 0 0 1640 1649 69 85 100 100 100 100 10126 10878 1.165 .858 .856 .826 .814 2.08 80 413 .878 .87 100 4470 8140 17 27 274 284 0 5934 230 5704 1.047 6349 6118 .955 1.044 .066 .062 .062
20 603 426 207 192 396 234 580 422 219 193 373 230 0 0 150 120 78 81 96 87 93 75 630 603 1.692 .591 .617 .502 .7 2.733 32 218 .56 .59 70 4630 8140 18 25 291 298 0 520 234 285 .721 515 280 1.388 .752 -.473 -.411 -.411

Total number of rows: 43008

Table truncated, full table size 9580 Kbytes.




Supplementary data files not provided
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