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Sample GSM93642 Query DataSets for GSM93642
Status Public on Jan 25, 2006
Title HUVEC exposure 1ug/ml colchicine 30'_1
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 1ug/ml colchicine 30'_1
Organism Homo sapiens
Characteristics 1ug/ml colchicine 30'_1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56592.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 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
1 332 145 111 69 221 76 339 143 113 72 228 74 0 0 79 44 24 26 100 89 100 69 297 302 2.908 .344 .325 .335 .35 2.131 65 355 .326 .66 100 1480 5820 113 123 75 85 0 244 116 128 .578 240 124 1.731 .545 -.792 -.875 -.875
2 4184 288 117 72 4067 216 4465 281 120 75 4348 209 0 0 1917 113 25 27 100 97 100 95 4283 4557 18.829 .053 .048 .053 .054 1.591 80 253 .049 .91 100 1630 5820 113 123 90 100 0 484 121 363 .089 472 351 11.21 .081 -3.487 -3.631 -3.631
3 3654 1630 121 72 3533 1558 3823 1555 125 75 3702 1483 0 0 1750 843 28 28 100 100 100 100 5091 5185 2.268 .441 .401 .437 .437 1.542 62 211 .434 .95 90 1770 5820 113 122 104 113 0 2738 121 2617 .741 2612 2491 1.35 .673 -.433 -.572 -.572
4 372 151 115 77 257 74 381 149 114 79 266 72 0 0 75 53 25 28 100 73 100 56 331 338 3.473 .288 .271 .264 .284 2.022 57 188 .289 .68 80 1920 5830 115 123 120 128 0 254 129 124 .484 250 121 2.068 .455 -1.048 -1.137 -1.137
5 494 392 107 75 387 317 537 391 110 78 430 316 0 0 145 148 22 27 98 97 97 97 704 746 1.221 .819 .735 .728 .837 2.245 72 309 .846 .89 100 2070 5820 113 123 134 144 0 658 126 532 1.376 657 531 .727 1.234 .46 .304 .304
6 268 124 109 72 159 52 258 118 112 75 149 46 0 0 43 36 23 27 100 76 100 36 211 195 3.058 .327 .309 .297 .331 1.971 46 212 .319 .5 80 2210 5820 114 122 149 157 0 208 121 87 .549 198 77 1.82 .519 -.864 -.947 -.947
7 914 761 105 72 809 689 989 769 107 73 884 697 0 0 355 357 25 25 100 100 98 100 1498 1581 1.174 .852 .788 .84 .809 1.725 73 297 .882 .94 100 2360 5820 113 123 163 173 0 1278 121 1157 1.43 1292 1171 .699 1.324 .517 .405 .405
8 431 252 104 74 327 178 435 246 106 76 331 172 0 0 115 84 22 27 98 94 98 94 505 503 1.837 .544 .52 .512 .592 2.097 59 218 .536 .83 90 2510 5820 113 122 178 187 0 423 124 299 .914 413 289 1.094 .873 -.129 -.196 -.196
9 238 112 107 68 131 44 240 108 110 73 133 40 0 0 41 33 28 28 100 67 97 33 175 173 2.977 .336 .301 .279 .348 3.024 74 266 .276 .39 110 2650 5820 112 123 191 202 0 188 114 74 .564 181 67 1.773 .505 -.826 -.985 -.985
10 1175 228 105 70 1070 158 1215 225 107 73 1110 155 0 0 377 86 21 25 100 96 100 88 1228 1265 6.772 .148 .14 .134 .134 1.793 118 289 .139 .83 120 2800 5820 112 124 206 218 0 383 118 265 .248 378 260 4.032 .235 -2.011 -2.092 -2.092
11 1726 111 106 69 1620 42 1844 107 106 73 1738 38 0 0 548 37 21 26 98 61 98 40 1662 1776 38.571 .026 .022 .024 .025 2.337 92 200 .024 .56 100 2940 5820 113 123 221 231 0 186 116 71 .044 180 64 22.964 .037 -4.521 -4.767 -4.767
12 1933 4023 105 71 1828 3952 2015 4313 105 76 1910 4242 0 0 837 1647 22 29 100 100 98 100 5780 6152 .463 2.162 2.221 2.415 2.171 2.126 95 247 2.183 .95 110 3090 5820 112 123 235 246 0 6757 119 6638 3.631 7244 7125 .275 3.73 1.86 1.899 1.899
13 1651 1972 107 71 1544 1901 1753 2023 108 74 1646 1952 0 0 542 656 22 26 100 100 100 100 3445 3598 .812 1.231 1.186 1.266 1.217 1.654 109 273 1.236 .95 110 3240 5810 111 122 250 261 0 3312 119 3193 2.068 3398 3279 .484 1.992 1.048 .994 .994
14 339 138 105 70 234 68 334 129 109 74 229 59 0 0 76 40 25 27 98 86 97 56 302 288 3.441 .291 .258 .244 .275 2.358 75 273 .253 .62 100 3380 5810 112 122 265 275 0 232 118 114 .488 217 99 2.049 .433 -1.035 -1.208 -1.208
15 461 106 105 74 356 32 475 105 110 77 370 31 0 0 97 29 25 30 100 50 100 15 388 401 11.125 .09 .084 .082 .093 2.486 64 166 .082 .43 90 3520 5830 114 123 279 288 0 178 124 54 .151 176 52 6.623 .141 -2.728 -2.829 -2.829
16 2455 2030 110 68 2345 1962 2782 2165 111 71 2672 2097 0 0 973 753 23 26 100 100 98 100 4307 4769 1.195 .837 .785 .9 .83 1.964 99 258 .813 .96 110 3670 5820 112 123 293 304 0 3410 114 3295 1.405 3636 3522 .712 1.318 .491 .399 .399
17 1463 2544 108 65 1355 2479 1606 2647 109 70 1498 2582 0 0 488 873 21 26 100 100 99 100 3834 4080 .547 1.83 1.724 1.952 1.862 1.653 100 235 1.859 .95 110 3820 5820 112 123 308 319 0 4273 109 4164 3.073 4446 4337 .325 2.895 1.62 1.534 1.534
18 753 208 108 71 645 137 768 203 111 75 660 132 0 0 230 81 33 27 98 94 98 88 782 792 4.708 .212 .2 .197 .203 1.908 131 345 .195 .76 130 3970 5810 110 123 322 335 0 349 119 230 .357 341 222 2.803 .336 -1.487 -1.574 -1.574
19 2937 2307 107 73 2830 2234 3092 2366 109 76 2985 2293 0 0 755 569 22 27 100 100 100 100 5064 5278 1.267 .789 .768 .807 .765 1.465 135 392 .762 .95 130 4120 5810 110 123 337 350 0 3875 123 3752 1.326 3974 3851 .754 1.29 .407 .368 .368
20 2467 1881 107 74 2360 1807 2748 2048 109 79 2641 1974 0 0 860 640 24 26 98 100 98 100 4167 4615 1.306 .766 .747 .795 .751 1.459 52 187 .717 .95 80 4250 5810 113 121 353 361 -50 3159 124 3035 1.286 3440 3316 .778 1.255 .363 .328

Total number of rows: 41472

Table truncated, full table size 9047 Kbytes.




Supplementary data files not provided
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