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Sample GSM93650 Query DataSets for GSM93650
Status Public on Jan 25, 2006
Title HUVEC exposure no colchicine 24 hr_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 no colchicine 24 hr_2
Organism Homo sapiens
Characteristics no colchicine 24 hr_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56612.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
1 369 244 100 81 269 163 380 231 103 84 280 150 0 0 76 63 22 26 100 100 100 98 432 430 1.65 .606 .536 .585 .564 1.665 66 228 .608 .81 90 1300 6480 59 68 57 66 0 286 95 191 .709 270 176 1.41 .627 -.495 -.673 -.673
2 6447 753 98 79 6349 674 6519 758 102 84 6421 679 0 0 2682 282 20 30 100 100 100 100 7023 7100 9.42 .106 .106 .108 .11 1.474 80 176 .098 .94 90 1430 6470 58 67 70 79 0 882 92 789 .124 887 795 8.046 .124 -3.008 -3.014 -3.014
3 3219 1489 98 81 3121 1408 3130 1422 101 85 3032 1341 0 0 1572 735 22 32 100 100 100 100 4529 4373 2.217 .451 .442 .443 .445 1.425 81 273 .445 .97 100 1590 6470 58 68 86 96 0 1743 95 1648 .528 1665 1570 1.893 .518 -.921 -.95 -.95
4 373 253 104 83 269 170 363 255 106 87 259 172 0 0 68 62 25 31 100 100 100 95 439 431 1.582 .632 .664 .606 .623 1.618 74 201 .619 .84 90 1730 6470 58 67 100 109 0 296 97 199 .74 299 201 1.352 .777 -.435 -.363 -.363
5 761 904 100 87 661 817 826 952 103 90 726 865 0 0 256 344 23 35 100 100 100 100 1478 1591 .809 1.236 1.191 1.226 1.173 1.408 81 249 1.263 .94 100 1880 6470 58 68 115 125 0 1058 102 956 1.447 1115 1013 .691 1.395 .533 .48 .48
6 273 224 97 84 176 140 265 209 99 86 168 125 0 0 70 110 22 31 98 97 98 87 316 293 1.257 .795 .744 .684 .668 2.223 71 201 1.052 .58 90 2020 6470 58 67 129 138 0 262 98 164 .931 245 146 1.074 .871 -.103 -.199 -.199
7 1010 1189 96 83 914 1106 1048 1248 99 88 952 1165 0 0 328 379 21 31 100 100 98 100 2020 2117 .826 1.21 1.224 1.257 1.215 1.565 80 265 1.205 .96 100 2180 6470 58 68 145 155 0 1392 97 1295 1.417 1461 1364 .706 1.433 .502 .519 .519
8 409 453 96 85 313 368 432 452 98 87 336 367 0 0 113 133 20 28 100 100 100 100 681 703 .851 1.176 1.092 1.194 1.186 1.464 81 261 1.196 .92 100 2320 6470 58 68 159 169 0 530 100 431 1.376 529 430 .727 1.279 .461 .355 .355
9 250 162 97 85 153 77 236 150 97 83 139 65 0 0 84 64 20 26 100 88 100 61 230 204 1.987 .503 .468 .465 .474 1.932 80 284 .482 .71 110 2470 6460 56 67 173 184 0 190 100 90 .589 176 76 1.697 .547 -.763 -.869 -.869
10 1667 473 95 83 1572 390 1682 459 98 85 1587 376 0 0 397 128 22 27 100 99 100 99 1962 1963 4.031 .248 .237 .239 .238 1.642 123 299 .237 .92 120 2610 6470 57 69 187 199 0 554 97 457 .29 537 440 3.443 .277 -1.784 -1.85 -1.85
11 3512 188 95 85 3417 103 3773 187 97 90 3678 102 0 0 911 53 26 41 100 89 100 60 3520 3780 33.175 .03 .028 .026 .03 2.105 93 212 .03 .78 100 2760 6470 58 68 203 213 0 220 100 121 .035 219 119 28.337 .032 -4.825 -4.945 -4.945
12 2309 7905 97 85 2212 7820 2410 8027 98 86 2313 7942 0 0 1005 3301 22 30 100 100 98 100 10032 10255 .283 3.535 3.434 3.78 3.486 1.611 92 207 3.538 .98 100 2910 6470 58 68 218 228 0 9255 100 9155 4.139 9397 9298 .242 4.02 2.049 2.007 2.007
13 2120 5427 99 87 2021 5340 2121 5474 101 90 2022 5387 0 0 839 1950 22 32 100 100 100 100 7361 7409 .378 2.642 2.664 2.878 2.62 1.706 109 322 2.658 .95 120 3050 6470 57 69 231 243 0 6353 102 6252 3.093 6409 6307 .323 3.119 1.629 1.641 1.641
14 346 212 96 86 250 126 345 204 98 86 249 118 0 0 73 58 19 28 98 97 97 93 376 367 1.984 .504 .474 .474 .482 1.667 90 243 .522 .83 100 3200 6460 57 67 247 257 0 248 101 148 .59 239 138 1.695 .555 -.761 -.85 -.85
15 718 161 95 85 623 76 724 163 99 87 629 78 0 0 182 48 20 26 100 82 100 65 699 707 8.197 .122 .124 .108 .137 2.358 80 224 .115 .7 100 3350 6470 58 68 262 272 0 188 100 89 .143 191 91 7.002 .145 -2.808 -2.784 -2.784
16 3893 3109 99 87 3794 3022 3941 3065 101 88 3842 2978 0 0 1416 1112 21 26 100 100 100 100 6816 6820 1.255 .797 .775 .828 .792 1.535 89 249 .785 .97 110 3500 6470 57 68 276 287 0 3640 102 3538 .933 3588 3486 1.072 .907 -.101 -.14 -.14
17 3010 5677 100 91 2910 5586 3326 5705 103 90 3226 5614 0 0 1160 2309 21 28 100 100 100 100 8496 8840 .521 1.92 1.74 2 1.853 1.63 100 214 1.962 .97 110 3640 6470 57 68 290 301 0 6646 107 6540 2.247 6679 6572 .445 2.037 1.168 1.027 1.027
18 1505 1960 99 91 1406 1869 1592 2015 102 94 1493 1924 0 0 414 560 19 29 99 100 99 100 3275 3417 .752 1.329 1.289 1.319 1.323 1.452 122 294 1.343 .95 120 3780 6460 56 68 304 316 0 2295 107 2188 1.556 2359 2252 .643 1.509 .638 .593 .593
19 3319 3918 99 87 3220 3831 3484 3831 100 90 3385 3744 0 0 1100 1256 22 27 100 100 100 100 7051 7129 .841 1.19 1.106 1.254 1.135 1.655 133 277 1.185 .95 120 3930 6470 57 69 319 331 0 4587 102 4485 1.393 4485 4383 .718 1.295 .478 .373 .373
20 3486 3799 97 85 3389 3714 3624 3900 100 88 3527 3815 0 0 1273 1329 24 28 99 100 98 100 7103 7342 .912 1.096 1.082 1.187 1.076 1.865 100 264 1.081 .97 110 4090 6460 56 67 335 346 0 4448 100 4348 1.283 4566 4466 .779 1.266 .36 .341 .341

Total number of rows: 41472

Table truncated, full table size 9058 Kbytes.




Supplementary data files not provided
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