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Sample GSM93630 Query DataSets for GSM93630
Status Public on Jan 25, 2006
Title Prostate - DU145
Sample type RNA
 
Channel 1
Source name DU145 control
Organism Homo sapiens
Characteristics DU145 control
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name DU145 1uM 5-aza-dC 3 days
Organism Homo sapiens
Characteristics DU145 1uM 5-aza-dC 3 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27547.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) array@genome.stanford.edu
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
1 613 596 125 161 488 435 564 505 134 166 439 344 0 0 347 282 41 67 88 94 84 86 923 783 1.122 .891 .784 .939 .828 2.544 52 276 .865 .87 80 1910 8010 35 43 19 27 0 655 177 478 .98 555 378 1.021 .861 -.03 -.216 -.216
2 391 297 130 162 261 135 420 307 135 166 290 145 0 0 113 118 41 64 94 65 90 57 396 435 1.933 .517 .5 .649 .568 2.36 52 269 .606 .47 80 2050 8000 34 42 33 41 0 326 178 148 .568 337 159 1.759 .549 -.815 -.864 -.864
3 1064 1151 137 164 927 987 1108 1223 170 189 971 1059 0 0 751 786 175 142 71 78 65 65 1914 2030 .939 1.065 1.091 1.106 1.062 2.244 32 169 1.031 .88 60 2190 8020 37 43 48 54 0 1265 180 1085 1.17 1344 1164 .855 1.198 .227 .261 .261
4 22265 27451 130 154 22135 27297 25661 31186 145 173 25531 31032 0 0 13143 15717 82 82 100 100 100 100 49432 56563 .811 1.233 1.215 1.43 1.251 2.847 32 224 1.244 .92 70 2340 8010 35 42 62 69 0 30166 169 29997 1.355 34270 34101 .738 1.336 .438 .418 .418
5 269 231 131 151 138 80 185 178 145 165 54 27 0 0 178 143 75 79 44 34 32 30 218 81 1.725 .58 .5 .984 1.005 3.655 52 274 .765 .56 80 2480 8000 34 42 76 84 -50 254 166 88 .637 196 30 1.57 .549 -.651 -.864
6 226 236 134 150 92 86 154 183 138 158 20 33 0 0 152 153 41 62 44 40 32 25 178 53 1.07 .935 1.65 1.046 1.119 3.312 52 294 1.035 .56 80 2630 8000 34 42 91 99 -50 259 165 95 1.027 201 36 .973 1.813 .039 .859
7 391 332 133 152 258 180 387 327 140 158 254 175 0 0 122 92 42 58 90 93 90 68 438 429 1.433 .698 .689 .678 .649 1.963 32 224 .768 .63 70 2780 8000 34 41 106 113 0 365 167 198 .767 359 192 1.304 .757 -.383 -.401 -.401
8 16995 22421 132 167 16863 22254 17634 24094 139 172 17502 23927 0 0 5563 8503 46 66 100 100 100 100 39117 41429 .758 1.32 1.367 1.277 1.318 2.096 52 339 1.4 .93 90 2930 8000 33 42 120 129 0 24638 184 24455 1.45 26477 26293 .69 1.502 .536 .587 .587
9 477 553 134 173 343 380 182 309 147 175 48 136 0 0 521 567 59 60 46 57 38 51 723 184 .903 1.108 2.833 1.114 1.057 3.062 52 274 1.124 .86 80 3070 8000 34 42 135 143 -50 608 190 418 1.217 340 149 .821 3.114 .284 1.639
10 222 190 132 159 90 31 153 163 143 164 21 4 0 0 151 96 55 59 38 30 28 13 121 25 2.903 .344 .19 .785 .792 4.371 52 267 .577 .39 80 3220 8000 34 42 150 158 -50 209 175 34 .379 179 4 2.642 .209 -1.402 -2.256
11 7657 8167 129 162 7528 8005 5128 8041 136 169 4999 7879 0 0 6042 6359 43 59 100 100 100 100 15533 12878 .94 1.063 1.576 1.002 .963 1.794 80 471 1.062 .86 110 3370 8000 32 43 163 174 0 8975 178 8797 1.169 8836 8658 .856 1.732 .225 .792 .792
12 3289 3686 131 160 3158 3526 3840 4075 137 168 3709 3915 0 0 1418 1113 37 65 96 100 96 100 6684 7624 .896 1.117 1.056 1.472 1.051 2.422 32 171 1.037 .95 60 3520 8010 36 42 181 187 0 4051 176 3875 1.227 4478 4302 .815 1.16 .295 .214 .214
13 1217 1634 132 161 1085 1473 1310 1736 137 171 1178 1575 0 0 647 808 38 69 96 96 92 94 2558 2753 .737 1.358 1.337 1.359 1.313 2.213 52 296 1.348 .91 80 3670 8010 35 43 195 203 0 1796 177 1619 1.492 1908 1731 .67 1.469 .577 .555 .555
14 595 387 131 160 464 227 575 365 136 169 444 205 0 0 159 140 40 59 100 91 100 75 691 649 2.044 .489 .462 .417 .418 2.066 12 104 .578 .74 50 3810 8000 35 40 210 215 0 425 176 249 .538 401 225 1.86 .507 -.895 -.979 -.979
15 15989 21343 133 177 15856 21166 17105 20311 139 187 16972 20134 0 0 9856 15051 45 68 98 98 96 97 37022 37106 .749 1.335 1.186 1.209 1.335 2.117 80 417 1.427 .95 100 3950 8000 33 43 222 232 0 23454 195 23259 1.467 22320 22125 .682 1.304 .553 .383 .383
16 3213 4023 131 180 3082 3843 3661 4273 135 185 3530 4093 0 0 1812 1903 39 65 100 98 100 94 6925 7623 .802 1.247 1.159 1.242 1.236 1.88 52 272 1.193 .94 80 4100 8000 34 42 238 246 0 4421 198 4223 1.37 4696 4498 .73 1.274 .454 .35 .35
17 352 152 132 164 220 -12 325 139 143 172 193 -25 0 0 101 47 51 73 100 8 91 0 208 168 null null null .142 .266 6.42 12 104 5.506 .04 50 4250 8000 35 40 254 259 0 167 180 -13 null 153 null null null null null null
18 368 208 138 156 230 52 372 208 142 163 234 52 0 0 78 78 45 62 100 43 96 18 282 286 4.423 .226 .222 .356 .375 2.686 32 196 .23 .25 70 4400 8010 35 42 268 275 0 229 171 57 .248 229 57 4.025 .244 -2.009 -2.034 -2.034
19 4317 4894 133 150 4184 4744 4618 5070 141 156 4485 4920 0 0 1450 1525 45 57 100 100 100 98 8928 9405 .882 1.134 1.097 1.163 1.072 1.814 80 415 1.126 .92 100 4540 8000 33 43 281 291 0 5378 165 5213 1.246 5571 5407 .803 1.205 .317 .27 .27
20 426 287 134 146 292 141 436 292 146 151 302 146 0 0 87 115 53 54 100 84 96 62 433 448 2.071 .483 .483 .456 .44 2.481 32 170 .57 .48 60 4690 8000 35 41 298 304 0 315 160 155 .531 321 160 1.885 .531 -.914 -.913 -.913

Total number of rows: 43008

Table truncated, full table size 9593 Kbytes.




Supplementary data files not provided
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