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Sample GSM93631 Query DataSets for GSM93631
Status Public on Jan 25, 2006
Title Prostate - PC3
Sample type RNA
 
Channel 1
Source name PC3 control
Organism Homo sapiens
Characteristics PC3 control
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PC3 1uM 5-aza-dC 4 days
Organism Homo sapiens
Characteristics PC3 1uM 5-aza-dC 4 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27548.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
1 297 266 105 119 192 147 297 262 112 129 192 143 0 0 65 83 34 48 100 90 96 75 339 335 1.306 .766 .745 .725 .755 2.032 32 226 .904 .62 70 1670 8490 15 22 29 36 0 277 124 153 .798 273 149 1.254 .776 -.326 -.366 -.366
2 248 180 103 116 145 64 259 176 110 125 156 60 0 0 63 55 37 49 92 59 84 26 209 216 2.266 .441 .385 .562 .521 3.375 52 285 .423 .33 80 1820 8490 15 23 44 52 0 188 121 67 .46 183 63 2.175 .401 -1.121 -1.32 -1.32
3 396 335 102 116 294 219 369 330 109 123 267 214 0 0 145 133 40 46 100 90 100 80 513 481 1.342 .745 .801 .681 .685 2.082 52 278 .781 .72 80 1960 8490 15 23 58 66 0 349 121 228 .776 344 223 1.289 .835 -.366 -.26 -.26
4 7657 11215 105 121 7552 11094 6492 10158 111 131 6387 10037 0 0 5169 6096 36 55 100 100 100 100 18646 16424 .681 1.469 1.571 1.513 1.552 2.254 32 220 2.138 .59 70 2100 8490 15 22 72 79 0 11682 126 11556 1.53 10581 10455 .653 1.637 .614 .711 .711
5 223 186 109 122 114 64 225 186 116 131 116 64 0 0 45 74 38 51 93 59 84 15 178 180 1.781 .561 .552 .608 .694 2.479 32 205 1.049 .27 70 2260 8490 15 22 88 95 0 194 127 67 .585 194 67 1.71 .575 -.774 -.799 -.799
6 135 126 110 118 25 8 120 126 116 131 10 8 0 0 57 47 43 68 30 11 13 0 33 18 3.125 .32 .8 1.079 1.22 4.924 52 260 23.324 .03 80 2390 8480 14 22 101 109 -50 131 123 8 .333 131 8 3 .833 -1.585 -.263
7 178 136 106 117 72 19 166 128 110 124 60 11 0 0 50 41 35 50 71 21 48 7 91 71 3.789 .264 .183 .459 .579 3.751 52 277 .82 .13 80 2540 8480 14 22 116 124 -50 142 122 20 .275 133 11 3.638 .191 -1.863 -2.389
8 11979 14950 102 113 11877 14837 11711 15325 107 122 11609 15212 0 0 3568 3694 35 46 100 100 100 100 26714 26821 .8 1.249 1.31 1.265 1.274 1.282 52 256 1.234 .94 80 2690 8490 15 23 131 139 0 15573 118 15455 1.301 15964 15846 .768 1.365 .38 .449 .449
9 324 355 107 115 217 240 346 333 113 125 239 218 0 0 110 173 41 47 90 90 90 81 457 457 .904 1.106 .912 1.135 1.193 2.972 32 200 1.383 .59 70 2830 8480 14 21 145 152 0 370 120 250 1.152 347 227 .868 .95 .204 -.074 -.074
10 146 132 102 113 44 19 140 123 110 123 38 10 0 0 61 52 39 63 50 19 25 5 63 48 2.316 .432 .263 .587 .652 3.656 52 268 .625 .25 80 2970 8480 14 22 159 167 -50 138 118 20 .45 128 10 2.223 .274 -1.153 -1.867
11 2795 3653 105 122 2690 3531 2989 3767 113 134 2884 3645 0 0 917 1845 37 95 100 96 98 93 6221 6529 .762 1.313 1.264 1.16 1.295 1.917 80 404 1.528 .88 100 3130 8480 13 23 174 184 0 3805 127 3678 1.367 3924 3797 .731 1.317 .451 .397 .397
12 595 513 103 129 492 384 525 473 113 134 422 344 0 0 303 166 42 50 100 100 100 100 876 766 1.281 .78 .815 .83 .852 1.799 32 213 .851 .52 70 3270 8490 15 22 189 196 0 534 134 400 .813 493 358 1.23 .849 -.299 -.236 -.236
13 408 479 101 126 307 353 404 442 109 136 303 316 0 0 161 183 35 65 90 100 90 90 660 619 .87 1.15 1.043 1.114 .881 2.307 32 212 .999 .69 70 3420 8480 14 21 204 211 0 499 131 368 1.198 460 329 .835 1.086 .26 .12 .12
14 163 171 107 129 56 42 152 163 114 137 45 34 0 0 68 62 40 60 51 34 36 11 98 79 1.333 .75 .756 .834 .712 2.912 52 286 2.359 .28 80 3560 8480 14 22 218 226 -50 178 134 44 .781 170 35 1.28 .787 -.356 -.345
15 11822 12443 105 127 11717 12316 12133 13363 111 137 12028 13236 0 0 3510 4680 33 59 100 100 100 100 24033 25264 .951 1.051 1.1 .958 1.051 1.798 52 302 1.119 .93 90 3710 8480 13 22 232 241 0 12961 132 12829 1.095 13920 13788 .913 1.146 .131 .197 .197
16 1114 1327 109 127 1005 1200 1193 1278 115 132 1084 1151 0 0 531 510 36 53 98 100 98 100 2205 2235 .838 1.194 1.062 1.318 1.288 1.729 52 264 1.137 .88 80 3850 8490 15 23 247 255 0 1382 132 1250 1.244 1331 1199 .804 1.106 .315 .145 .145
17 318 141 144 126 174 15 310 134 521 131 166 8 0 0 61 45 3766 42 0 25 0 8 189 174 11.6 .086 .048 .242 .295 2.529 12 104 .145 .17 50 4010 8490 16 21 264 269 0 147 131 16 .09 140 8 11.136 .05 -3.477 -4.316 -4.316
18 202 119 125 132 77 -13 204 116 2130 897 79 -16 0 0 73 56 10778 5808 0 0 0 0 64 63 null null null .507 .486 4.231 52 263 -1 -1 80 4140 8480 14 22 276 284 -50 124 138 -14 null 121 null null null null null
19 3175 4069 120 117 3055 3952 3208 4194 125 124 3088 4077 0 0 871 1337 39 47 100 100 100 100 7007 7165 .773 1.294 1.32 1.241 1.364 1.674 80 393 1.386 .88 100 4290 8480 13 23 290 300 0 4239 122 4117 1.348 4369 4247 .742 1.375 .43 .46 .46
20 250 174 122 108 128 66 257 169 132 116 135 61 0 0 66 53 41 38 93 65 75 34 194 196 1.939 .516 .452 .441 .607 3.793 32 191 .487 .32 70 4430 8490 15 22 305 312 0 181 113 69 .537 176 64 1.862 .471 -.897 -1.087 -1.087

Total number of rows: 43008

Table truncated, full table size 9303 Kbytes.




Supplementary data files not provided
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