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Sample GSM91920 Query DataSets for GSM91920
Status Public on Jan 12, 2006
Title DU145vsCRG
Sample type RNA
 
Channel 1
Source name CRG mRNA
Organism Homo sapiens
Characteristics CRG mRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name DU145 total RNA
Organism Homo sapiens
Characteristics DU145 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35463.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 11, 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 GPL3341
Series (2)
GSE4016 Gene expression variations in prostate cancer cell lines
GSE4396 Genome-wide characterization of gene expression variations and DNA copy number changes in 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 1420 519 274 108 1146 411 1399 518 290 113 1125 410 0 0 476 255 93 42 100 100 98 94 1557 1535 2.788 .359 .364 .319 .363 1.874 52 232 .352 .83 80 1490 9320 40 48 13 21 0 564 117 447 .39 563 446 2.565 .396 -1.359 -1.336 -1.336
2 8766 883 278 111 8488 772 9660 898 284 114 9382 787 0 0 2998 343 77 44 100 100 100 98 9260 10169 10.995 .091 .084 .087 .088 1.474 52 253 .088 .92 80 1630 9310 39 47 27 35 0 960 121 839 .099 976 855 10.115 .091 -3.338 -3.455 -3.455
3 3729 2286 270 106 3459 2180 3604 2288 276 109 3334 2182 0 0 1431 923 75 41 100 100 100 100 5639 5516 1.587 .63 .654 .627 .66 1.465 32 165 .611 .91 60 1780 9310 40 46 43 49 0 2485 115 2370 .685 2487 2372 1.46 .711 -.546 -.491 -.491
4 1330 996 271 103 1059 893 1296 1014 276 110 1025 911 0 0 578 338 71 45 98 100 96 100 1952 1936 1.186 .843 .889 .969 .89 1.935 52 245 .748 .89 80 1920 9310 39 47 56 64 0 1083 112 971 .917 1102 990 1.091 .966 -.126 -.05 -.05
5 2698 2273 277 109 2421 2164 2714 2329 285 116 2437 2220 0 0 1042 666 87 45 100 100 100 100 4585 4657 1.119 .894 .911 .977 .841 1.601 52 262 .815 .94 80 2060 9310 39 47 70 78 0 2471 118 2352 .972 2532 2413 1.029 .99 -.042 -.014 -.014
6 1544 957 282 118 1262 839 1453 868 285 123 1171 750 0 0 490 348 88 49 100 100 100 100 2101 1921 1.504 .665 .64 .656 .693 1.616 32 204 .635 .85 70 2220 9310 39 46 86 93 0 1040 128 912 .723 943 815 1.384 .696 -.469 -.522 -.522
7 3107 3015 274 113 2833 2902 3242 3217 279 117 2968 3104 0 0 1135 902 70 44 100 100 100 100 5735 6072 .976 1.024 1.046 1.072 1.031 1.369 52 257 .969 .95 80 2360 9310 39 47 100 108 0 3277 123 3154 1.113 3497 3374 .898 1.137 .155 .185 .185
8 1723 3403 264 113 1459 3290 1749 3607 273 117 1485 3494 0 0 644 1071 73 46 100 100 100 100 4749 4979 .443 2.255 2.353 2.394 2.372 1.364 52 275 2.206 .94 90 2500 9310 38 47 113 122 0 3699 123 3576 2.451 3921 3798 .408 2.557 1.293 1.355 1.355
9 1389 451 268 117 1121 334 1414 436 275 123 1146 319 0 0 450 204 77 47 98 91 97 85 1455 1465 3.356 .298 .278 .249 .296 2.088 80 365 .301 .88 100 2650 9310 38 48 128 138 0 490 127 363 .324 474 347 3.088 .303 -1.627 -1.725 -1.725
10 1119 554 271 121 848 433 1043 535 277 125 772 414 0 0 335 197 74 48 100 100 100 100 1281 1186 1.958 .511 .536 .496 .488 1.582 32 206 .488 .83 70 2800 9300 38 45 144 151 0 602 132 471 .555 582 450 1.802 .583 -.849 -.779 -.779
11 5640 784 263 118 5377 666 5591 796 269 121 5328 678 0 0 1161 209 74 45 100 100 100 100 6043 6006 8.074 .124 .127 .12 .125 1.337 52 301 .117 .93 90 2950 9300 37 46 158 167 0 852 128 724 .135 865 737 7.428 .138 -2.893 -2.854 -2.854
12 5302 8082 266 117 5036 7965 5756 8704 292 141 5490 8587 0 0 3997 5124 176 153 90 100 84 100 13001 14077 .632 1.582 1.564 2.181 1.664 2.206 52 245 1.51 .94 80 3080 9300 38 46 172 180 0 8785 127 8658 1.719 9461 9334 .582 1.7 .782 .766 .766
13 2038 766 270 123 1768 643 2056 761 294 140 1786 638 0 0 538 173 170 138 100 100 100 100 2411 2424 2.75 .364 .357 .37 .37 1.412 52 321 .342 .87 90 3230 9300 37 46 186 195 0 833 134 699 .395 827 693 2.53 .388 -1.339 -1.365 -1.365
14 1106 241 272 123 834 118 1147 243 288 126 875 120 0 0 285 64 100 51 100 80 100 63 952 995 7.068 .141 .137 .126 .144 2.047 52 326 .129 .68 90 3390 9300 37 46 202 211 0 262 134 128 .154 264 130 6.502 .149 -2.701 -2.746 -2.746
15 2519 532 278 123 2241 409 2581 543 280 125 2303 420 0 0 519 145 68 46 100 100 100 100 2650 2723 5.479 .183 .182 .174 .191 1.402 52 264 .168 .88 90 3530 9300 37 46 216 225 0 578 134 445 .198 590 457 5.041 .198 -2.334 -2.335 -2.335
16 10782 31984 274 129 10508 31855 11354 33108 348 305 11080 32979 0 0 3789 8924 646 1326 98 100 98 100 42363 44059 .33 3.031 2.976 3.221 3.073 1.499 52 308 2.896 .96 90 3660 9300 37 46 229 238 0 34765 140 34625 3.295 35987 35847 .303 3.235 1.72 1.694 1.694
17 4760 4685 269 134 4491 4551 4995 4710 521 337 4726 4576 0 0 1438 1406 1434 1409 98 100 86 90 9042 9302 .987 1.013 .968 1.028 1.031 1.325 52 270 1 .96 80 3820 9300 38 46 246 254 0 5092 146 4947 1.101 5120 4974 .908 1.052 .139 .074 .074
18 396 189 261 127 135 62 297 128 437 145 36 1 0 0 295 148 1336 116 1 21 0 11 197 37 2.177 .459 .028 .684 .52 3.632 52 239 .05 .56 80 3980 9290 37 45 262 270 -50 205 138 67 .499 139 1 2.003 .03 -1.002 -5.05
19 3876 13536 258 131 3618 13405 4333 15435 271 136 4075 15304 0 0 1571 4552 94 54 98 100 98 100 17023 19379 .27 3.705 3.756 4.103 3.807 1.723 80 344 3.649 .95 100 4110 9300 37 47 274 284 0 14713 142 14571 4.027 16777 16635 .248 4.082 2.01 2.029 2.029
20 3519 2952 267 131 3252 2821 3656 2971 271 135 3389 2840 0 0 969 674 66 53 100 100 100 100 6073 6229 1.153 .867 .838 .891 .84 1.429 52 289 .814 .93 90 4270 9300 37 46 290 299 0 3209 142 3066 .943 3229 3087 1.061 .911 -.085 -.135 -.135

Total number of rows: 43104

Table truncated, full table size 9731 Kbytes.




Supplementary data files not provided
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