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Sample GSM93649 Query DataSets for GSM93649
Status Public on Jan 25, 2006
Title HUVEC exposure no colchicine 0_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 no colchicine 0_2
Organism Homo sapiens
Characteristics no colchicine 0_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56587.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
1 315 150 96 61 219 89 316 140 97 65 220 79 0 0 86 63 20 22 100 91 97 80 308 299 2.461 .406 .359 .374 .361 2.394 72 252 .395 .69 90 1400 6390 54 63 59 68 0 190 77 113 .515 177 100 1.941 .455 -.957 -1.135 -1.135
2 4761 349 95 63 4666 286 5348 354 95 65 5253 291 0 0 2693 163 20 24 100 97 100 97 4952 5544 16.315 .061 .055 .064 .061 1.52 81 276 .056 .92 110 1560 6390 53 64 74 85 0 442 80 363 .078 449 369 12.869 .07 -3.686 -3.832 -3.832
3 2597 1875 92 62 2505 1813 2736 1823 94 63 2644 1761 0 0 1521 1064 19 22 100 100 100 100 4318 4405 1.382 .724 .666 .741 .711 1.488 71 216 .709 .98 90 1700 6380 53 62 89 98 0 2377 79 2298 .918 2311 2233 1.09 .844 -.124 -.244 -.244
4 299 202 95 63 204 139 295 190 96 66 200 127 0 0 82 75 20 23 98 96 98 90 343 327 1.468 .681 .635 .634 .718 1.74 66 233 .711 .81 90 1850 6380 53 62 104 113 0 256 80 176 .864 241 161 1.158 .805 -.211 -.313 -.313
5 566 952 99 65 467 887 612 918 99 66 513 853 0 0 199 420 22 22 100 100 100 100 1354 1366 .526 1.899 1.663 1.87 1.961 1.385 72 229 1.972 .97 90 1990 6380 53 62 118 127 0 1207 82 1125 2.408 1164 1081 .415 2.108 1.268 1.076 1.076
6 277 163 101 64 176 99 284 156 102 67 183 92 0 0 51 60 27 25 98 96 98 87 275 275 1.778 .563 .503 .512 .525 2.127 54 194 .588 .7 80 2140 6390 55 63 134 142 0 207 81 126 .713 198 117 1.402 .637 -.488 -.65 -.65
7 1001 2038 103 74 898 1964 909 1793 135 167 806 1719 0 0 567 1311 223 583 89 88 75 65 2862 2525 .457 2.187 2.133 2.243 2.139 1.628 102 232 2.467 .9 100 2290 6380 53 63 148 158 0 2584 94 2490 2.773 2273 2179 .361 2.704 1.471 1.435 1.435
8 394 354 101 70 293 284 401 356 103 75 300 286 0 0 86 101 24 41 100 100 100 98 577 586 1.032 .969 .953 .951 .95 1.382 71 186 1.016 .89 90 2430 6390 54 63 162 171 0 449 89 360 1.229 451 363 .814 1.209 .297 .273 .273
9 229 123 99 67 130 56 223 113 108 78 124 46 0 0 50 49 100 76 78 26 8 7 186 170 2.321 .431 .371 .326 .375 2.635 84 246 .156 .37 110 2590 6390 53 64 177 188 0 156 85 71 .546 143 58 1.831 .47 -.873 -1.088 -1.088
10 1380 287 102 74 1278 213 1379 259 286 446 1277 185 0 0 483 128 1504 3645 27 0 0 0 1491 1462 6 .167 .145 .161 .145 1.615 132 339 .17 .75 130 2730 6380 51 64 190 203 0 364 94 270 .211 328 235 4.733 .184 -2.243 -2.445 -2.445
11 1938 143 107 78 1831 65 2063 115 363 600 1956 37 0 0 538 132 1781 4249 66 0 0 0 1896 1993 28.169 .035 .019 .025 .022 3.011 103 251 .041 .43 110 2870 6380 52 63 205 216 0 181 99 82 .045 146 47 22.22 .024 -4.474 -5.382 -5.382
12 1949 5835 101 70 1848 5765 2120 6742 107 74 2019 6672 0 0 788 2346 44 31 100 100 100 100 7613 8691 .321 3.12 3.305 3.172 3.143 1.455 94 271 3.144 .98 110 3010 6380 52 63 219 230 0 7397 89 7309 3.955 8547 8459 .253 4.189 1.984 2.067 2.067
13 1977 3813 98 69 1879 3744 2076 3785 100 72 1978 3716 0 0 572 1173 22 25 100 100 100 100 5623 5694 .502 1.993 1.879 2 2.014 1.237 104 259 2.024 .98 110 3160 6380 52 63 234 245 0 4834 87 4747 2.526 4799 4711 .396 2.382 1.337 1.252 1.252
14 330 181 101 73 229 108 334 167 102 75 233 94 0 0 88 60 23 25 98 98 98 90 337 327 2.12 .472 .403 .444 .387 2.123 93 227 1.815 .93 110 3300 6380 52 63 248 259 0 229 93 137 .598 212 119 1.673 .511 -.742 -.967 -.967
15 644 228 104 74 540 154 638 166 109 81 534 92 0 0 298 195 46 60 99 64 96 39 694 626 3.506 .285 .172 .217 .205 3.681 109 219 3.575 .51 110 3440 6380 52 63 262 273 0 289 94 195 .362 210 117 2.766 .218 -1.468 -2.195 -2.195
16 3107 2791 100 70 3007 2721 3328 2983 102 72 3228 2913 0 0 1053 948 23 26 100 100 100 100 5728 6141 1.105 .905 .902 .912 .903 1.268 97 227 .899 .98 100 3600 6380 53 63 279 289 0 3538 89 3450 1.147 3782 3693 .872 1.144 .198 .194 .194
17 2052 5185 98 70 1954 5115 2096 5628 100 73 1998 5558 0 0 716 1527 22 27 100 100 100 100 7069 7556 .382 2.618 2.782 2.738 2.647 1.475 110 242 2.638 .95 110 3740 6380 52 63 292 303 0 6573 89 6485 3.319 7135 7046 .301 3.527 1.731 1.818 1.818
18 2212 1882 98 71 2114 1811 2263 1929 99 74 2165 1858 0 0 758 723 22 27 100 100 100 100 3925 4023 1.167 .857 .858 .854 .841 1.607 138 332 .919 .91 130 3900 6380 51 64 307 320 0 2386 90 2296 1.086 2446 2356 .921 1.088 .119 .122 .122
19 3403 4628 99 71 3304 4557 3621 5010 103 74 3522 4939 0 0 1148 1530 33 26 100 100 100 100 7861 8461 .725 1.379 1.402 1.398 1.379 1.412 99 320 1.374 .97 120 4040 6370 51 63 322 334 0 5867 90 5777 1.749 6352 6262 .572 1.778 .806 .83 .83
20 3256 3663 98 70 3158 3593 3476 3830 102 73 3378 3760 0 0 1023 1108 38 27 100 100 100 100 6751 7138 .879 1.138 1.113 1.156 1.101 1.322 113 214 1.154 .96 100 4170 6380 53 63 336 346 0 4644 89 4555 1.442 4856 4767 .693 1.411 .528 .497 .497

Total number of rows: 41472

Table truncated, full table size 9104 Kbytes.




Supplementary data files not provided
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