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Sample GSM93635 Query DataSets for GSM93635
Status Public on Jan 25, 2006
Title HUVEC exposure no colchicine 0_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 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/2004-10/56588.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
1 404 232 135 86 269 146 399 223 137 90 264 137 0 0 108 84 30 31 100 97 98 82 415 401 1.842 .543 .519 .5 .503 2.249 81 343 .516 .71 100 1380 5640 95 105 65 75 0 326 121 205 .764 314 193 1.309 .73 -.389 -.454 -.454
2 4609 301 135 77 4474 224 4965 297 135 79 4830 220 0 0 2494 152 26 29 100 91 100 87 4698 5050 19.973 .05 .046 .046 .045 2.057 81 248 .044 .82 100 1530 5650 96 106 80 90 0 424 108 315 .07 418 310 14.195 .064 -3.827 -3.964 -3.964
3 2097 1028 131 79 1966 949 2163 1086 133 83 2032 1007 0 0 1154 519 26 30 100 100 100 100 2915 3039 2.072 .483 .496 .505 .464 1.907 74 213 .443 .91 90 1680 5640 95 104 95 104 0 1446 111 1335 .679 1528 1417 1.472 .697 -.558 -.52 -.52
4 499 170 132 85 367 85 491 161 134 85 359 76 0 0 118 50 27 28 100 93 100 67 452 435 4.318 .232 .212 .203 .222 2.11 61 212 .223 .68 90 1820 5650 96 105 109 118 0 239 120 120 .326 227 107 3.069 .298 -1.618 -1.747 -1.747
5 430 486 129 79 301 407 438 472 132 84 309 393 0 0 133 170 30 37 97 98 95 98 708 702 .74 1.352 1.272 1.309 1.288 1.742 73 293 1.382 .88 100 1970 5640 95 105 124 134 0 684 111 573 1.903 664 553 .526 1.79 .928 .84 .84
6 291 138 126 78 165 60 292 132 131 85 166 54 0 0 56 50 32 37 98 62 96 34 225 220 2.75 .364 .325 .295 .353 3.258 58 242 .367 .41 90 2110 5640 95 104 138 147 0 194 110 84 .512 186 76 1.954 .458 -.967 -1.128 -1.128
7 623 710 123 79 500 631 647 753 126 83 524 674 0 0 203 279 27 27 100 100 98 98 1131 1198 .792 1.262 1.286 1.215 1.188 1.886 70 291 1.322 .9 100 2260 5640 95 105 153 163 0 999 111 888 1.776 1059 948 .563 1.81 .828 .856 .856
8 335 206 128 82 207 124 338 200 138 84 210 118 0 0 109 75 44 28 93 94 92 82 331 328 1.669 .599 .562 .551 .554 2.63 75 263 .578 .73 90 2400 5630 94 103 167 176 0 290 115 174 .843 281 166 1.186 .791 -.247 -.339 -.339
9 406 141 133 88 273 53 401 132 144 92 268 44 0 0 175 44 51 34 88 57 82 30 326 312 5.151 .194 .164 .229 .228 2.965 52 211 .18 .54 80 2580 5640 96 104 186 194 -50 198 124 75 .273 186 62 3.661 .231 -1.872 -2.114
10 812 193 130 84 682 109 830 182 139 90 700 98 0 0 254 70 49 33 98 90 98 71 791 798 6.257 .16 .14 .145 .148 1.899 113 401 .154 .76 120 2690 5640 94 106 195 207 0 272 118 153 .225 256 138 4.447 .197 -2.153 -2.344 -2.344
11 1250 245 129 86 1121 159 1346 182 144 97 1217 96 0 0 450 166 65 52 97 68 97 49 1280 1313 7.05 .142 .079 .097 .102 4.003 104 278 .113 .5 110 2840 5640 94 105 210 221 0 345 121 224 .2 256 135 5.011 .111 -2.325 -3.172 -3.172
12 1814 4895 127 85 1687 4810 1979 5346 137 92 1852 5261 0 0 695 1910 49 43 96 100 96 100 6497 7113 .351 2.851 2.841 2.857 2.871 1.703 102 233 2.943 .95 100 2980 5640 95 105 225 235 0 6887 120 6768 4.012 7522 7402 .249 3.997 2.004 1.999 1.999
13 1787 2885 125 83 1662 2802 1880 2876 129 85 1755 2793 0 0 790 1284 29 26 98 100 97 100 4464 4548 .593 1.686 1.591 1.742 1.827 2.355 103 272 1.788 .87 110 3120 5640 94 105 238 249 0 4059 117 3942 2.372 4047 3930 .422 2.239 1.246 1.163 1.163
14 339 286 126 84 213 202 338 245 129 86 212 161 0 0 114 205 26 25 95 97 91 93 415 373 1.054 .948 .759 .806 .794 2.573 99 371 1.498 .77 120 3260 5630 93 105 252 264 0 402 118 284 1.334 345 227 .749 1.069 .416 .096 .096
15 438 128 124 83 314 45 426 121 128 89 302 38 0 0 90 43 28 52 100 32 100 9 359 340 6.978 .143 .126 .141 .162 2.259 73 224 .13 .29 100 3410 5640 95 105 268 278 0 180 117 63 .202 170 53 4.959 .177 -2.31 -2.498 -2.498
16 2502 2274 124 80 2378 2194 2624 2185 126 86 2500 2105 0 0 964 905 29 51 99 100 98 100 4572 4605 1.084 .923 .842 1.001 .921 2.522 102 250 .911 .89 110 3570 5640 94 105 283 294 0 3200 113 3087 1.298 3074 2962 .77 1.185 .376 .245 .245
17 1419 3073 126 81 1293 2992 1479 3190 128 84 1353 3109 0 0 592 1193 26 28 100 100 97 100 4285 4462 .432 2.314 2.298 2.596 2.285 2.641 108 257 2.454 .87 110 3710 5630 93 104 297 308 0 4324 114 4210 3.256 4488 4374 .307 3.233 1.703 1.693 1.693
18 831 339 130 82 701 257 847 325 131 87 717 243 0 0 270 138 32 28 98 98 97 98 958 960 2.728 .367 .339 .362 .334 1.808 141 344 .374 .64 130 3870 5630 92 105 312 325 0 477 115 362 .516 457 342 1.939 .477 -.955 -1.068 -1.068
19 2471 3444 125 84 2346 3360 2621 3324 139 96 2496 3240 0 0 791 1341 111 78 97 100 96 100 5706 5736 .698 1.432 1.298 1.569 1.336 2.269 138 520 1.507 .9 140 4030 5630 92 106 328 342 0 4846 118 4728 2.015 4677 4559 .496 1.826 1.011 .869 .869
20 2185 2775 122 87 2063 2688 2214 2659 152 113 2092 2572 0 0 770 894 186 125 98 100 98 98 4751 4664 .767 1.303 1.229 1.38 1.284 1.962 52 166 1.238 .89 80 4140 5630 95 103 342 350 -50 3904 122 3782 1.833 3741 3619 .545 1.73 .874 .791

Total number of rows: 41472

Table truncated, full table size 9065 Kbytes.




Supplementary data files not provided
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