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Sample GSM93639 Query DataSets for GSM93639
Status Public on Jan 25, 2006
Title HUVEC exposure 1 ug/ml colchicine 120'_2
Sample type RNA
 
Channel 1
Source name Stratagene reference
Organism Homo sapiens
Characteristics Stratagene reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 ug/ml colchicine 120'_2
Organism Homo sapiens
Characteristics 1 ug/ml colchicine 120'_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56598.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 GPL3386
Series (1)
GSE4090 Mechanism of the anti-inflammatory effect of colchicine in rheumatic diseases

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
1 269 175 124 96 145 79 266 168 126 101 142 72 0 0 64 61 27 34 100 74 94 52 224 214 1.835 .545 .507 .456 .513 3.038 50 231 .59 .56 80 1580 6010 77 85 86 94 0 201 110 91 .626 193 83 1.598 .582 -.676 -.78 -.78
2 4015 398 128 96 3887 302 4045 389 129 105 3917 293 0 0 1270 112 26 45 100 100 100 95 4189 4210 12.871 .078 .075 .076 .077 1.56 70 207 .07 .87 90 1720 6010 76 85 99 108 0 457 110 347 .089 447 337 11.206 .086 -3.486 -3.541 -3.541
3 2316 1977 116 95 2200 1882 2263 1603 119 106 2147 1508 0 0 1134 1150 28 39 100 100 100 100 4082 3655 1.169 .855 .702 .85 .764 1.499 72 231 .892 .93 90 1860 6010 76 85 113 122 0 2271 109 2162 .983 1841 1732 1.018 .807 -.025 -.31 -.31
4 275 232 111 91 164 141 273 221 113 99 162 130 0 0 50 56 24 37 100 95 100 93 305 292 1.163 .86 .802 .814 .93 1.677 46 213 .915 .77 80 2020 6010 77 85 130 138 0 266 105 162 .987 254 149 1.013 .922 -.018 -.118 -.118
5 469 481 108 90 361 391 478 465 109 95 370 375 0 0 135 138 24 40 100 100 100 100 752 745 .923 1.083 1.014 1.106 1.042 1.495 73 249 1.067 .91 90 2160 6010 76 85 143 152 0 552 103 449 1.244 534 431 .804 1.164 .315 .219 .219
6 236 194 112 101 124 93 220 188 115 107 108 87 0 0 67 59 30 44 100 80 90 48 217 195 1.333 .75 .806 .755 .92 2.325 31 157 .844 .56 70 2330 6000 76 83 161 168 0 223 116 107 .861 216 100 1.161 .925 -.215 -.112 -.112
7 728 816 110 92 618 724 791 872 112 96 681 780 0 0 213 207 29 31 100 100 100 100 1342 1461 .854 1.172 1.145 1.203 1.163 1.284 67 231 1.144 .96 90 2460 6010 76 85 173 182 0 937 106 832 1.346 1002 896 .743 1.315 .428 .396 .396
8 272 434 108 90 164 344 269 426 112 96 161 336 0 0 56 122 29 31 100 100 96 100 508 497 .477 2.098 2.087 2.114 2.154 1.481 66 257 2.19 .88 90 2600 6010 76 85 187 196 0 498 103 395 2.409 489 386 .415 2.397 1.268 1.261 1.261
9 206 144 114 96 92 48 208 145 117 101 94 49 0 0 37 35 28 38 93 53 84 31 140 143 1.917 .522 .521 .487 .513 2.594 32 203 .663 .41 80 2760 6010 77 85 204 212 0 165 110 55 .599 167 56 1.669 .599 -.739 -.74 -.74
10 915 198 113 90 802 108 929 194 117 93 816 104 0 0 206 59 26 32 100 89 100 74 910 920 7.426 .135 .127 .115 .13 2.181 93 268 .124 .71 110 2900 6010 75 86 216 227 0 227 103 124 .155 223 119 6.466 .146 -2.693 -2.772 -2.772
11 2090 567 111 95 1979 472 2007 167 112 98 1896 72 0 0 836 878 23 32 100 73 100 53 2451 1968 4.193 .239 .038 .072 .048 5.515 99 279 .365 .57 110 3050 6010 75 86 231 242 0 651 109 542 .274 192 83 3.651 .044 -1.868 -4.519 -4.519
12 1211 3505 113 99 1098 3406 1327 3539 114 104 1214 3440 0 0 385 984 23 46 100 100 100 100 4504 4654 .322 3.102 2.834 3.225 3.053 1.29 85 252 3.062 .97 100 3200 6010 76 86 247 257 0 4026 114 3912 3.563 4065 3951 .281 3.254 1.833 1.702 1.702
13 1480 2426 115 92 1365 2334 1512 2363 117 98 1397 2271 0 0 538 783 27 42 100 100 100 100 3699 3668 .585 1.71 1.626 1.797 1.656 1.513 102 307 1.684 .96 110 3340 6010 75 86 260 271 0 2786 106 2681 1.964 2714 2608 .509 1.867 .974 .901 .901
14 256 163 116 97 140 66 250 152 118 99 134 55 0 0 54 66 25 30 100 65 97 39 206 189 2.121 .471 .41 .396 .554 2.721 38 206 .513 .48 80 3490 6000 76 84 277 285 0 187 111 76 .541 175 63 1.847 .471 -.885 -1.085 -1.085
15 485 134 122 94 363 40 478 129 125 97 356 35 0 0 86 40 25 30 100 53 100 21 403 391 9.075 .11 .098 .103 .112 2.576 65 207 .09 .36 90 3640 6000 75 84 291 300 0 154 108 46 .127 148 40 7.901 .113 -2.982 -3.147 -3.147
16 1879 1979 125 96 1754 1883 1929 1971 131 107 1804 1875 0 0 625 656 67 67 100 100 100 100 3637 3679 .931 1.074 1.039 1.09 1.081 1.409 96 276 1.07 .96 110 3790 6010 75 86 305 316 0 2273 110 2163 1.233 2264 2153 .811 1.194 .302 .255 .255
17 1510 2951 122 98 1388 2853 1610 3011 129 109 1488 2913 0 0 443 886 75 72 100 100 100 100 4241 4401 .487 2.055 1.958 2.118 2.052 1.387 91 218 2.084 .97 100 3930 6010 76 86 320 330 0 3389 113 3277 2.361 3458 3346 .424 2.248 1.239 1.169 1.169
18 1142 396 118 93 1024 303 1150 378 120 98 1032 285 0 0 227 116 26 32 100 100 100 100 1327 1317 3.38 .296 .276 .282 .293 1.469 110 221 .288 .88 110 4080 6010 75 86 334 345 0 455 107 348 .34 434 327 2.942 .317 -1.557 -1.657 -1.657
19 2017 2767 116 100 1901 2667 2132 2857 119 103 2016 2757 0 0 580 725 24 33 100 100 100 100 4568 4773 .713 1.403 1.368 1.449 1.37 1.633 112 296 1.407 .95 120 4220 6010 75 87 348 360 0 3178 115 3063 1.611 3281 3166 .621 1.571 .688 .651 .651
20 2348 2577 112 101 2236 2476 2411 2535 115 106 2299 2434 0 0 661 700 26 36 100 100 100 100 4712 4733 .903 1.107 1.059 1.12 1.118 1.407 101 260 1.102 .96 110 4370 6010 75 86 363 374 0 2960 116 2844 1.272 2912 2796 .786 1.216 .347 .282 .282

Total number of rows: 41472

Table truncated, full table size 9035 Kbytes.




Supplementary data files not provided
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