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Sample GSM93640 Query DataSets for GSM93640
Status Public on Jan 25, 2006
Title HUVEC exposure 1 ug/ml colchicine 12hr_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 12hr_2
Organism Homo sapiens
Characteristics 1 ug/ml colchicine 12hr_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56608.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
1 461 250 122 84 339 166 455 236 124 89 333 152 0 0 96 94 28 36 100 94 100 86 505 485 2.042 .49 .456 .431 .467 1.832 67 274 .516 .81 90 1320 6580 69 78 59 68 0 308 104 205 .603 291 187 1.657 .562 -.729 -.83 -.83
2 7948 522 119 86 7829 436 8599 517 121 90 8480 431 0 0 3141 215 24 31 100 98 100 98 8265 8911 17.956 .056 .051 .056 .054 1.503 78 251 .052 .9 100 1480 6580 69 79 75 85 0 643 106 537 .069 637 531 14.572 .063 -3.865 -3.997 -3.997
3 4270 2034 114 85 4156 1949 4191 1883 117 86 4077 1798 0 0 2172 1246 23 29 100 100 100 100 6105 5875 2.132 .469 .441 .455 .442 1.366 78 260 .487 .96 100 1620 6580 69 79 89 99 0 2506 105 2402 .578 2320 2216 1.73 .543 -.791 -.88 -.88
4 474 233 117 82 357 151 476 223 118 85 359 141 0 0 91 68 24 27 100 98 100 95 508 500 2.364 .423 .393 .387 .396 1.662 63 195 .432 .84 90 1770 6580 69 78 104 113 0 287 101 186 .521 275 174 1.919 .484 -.94 -1.047 -1.047
5 1335 1518 117 88 1218 1430 1401 1491 120 92 1284 1403 0 0 446 555 22 28 100 100 100 100 2648 2687 .852 1.174 1.093 1.173 1.194 1.445 79 251 1.191 .95 100 1910 6580 69 79 118 128 0 1871 108 1762 1.447 1837 1729 .691 1.346 .533 .429 .429
6 378 213 116 83 262 130 379 203 118 85 263 120 0 0 86 67 22 28 100 98 98 94 392 383 2.015 .496 .456 .468 .501 1.904 68 222 .496 .78 90 2060 6570 68 77 133 142 0 262 102 160 .611 250 148 1.636 .562 -.71 -.831 -.831
7 1598 1921 116 82 1482 1839 1727 1903 118 87 1611 1821 0 0 605 798 22 30 100 100 100 100 3321 3432 .806 1.241 1.13 1.269 1.244 1.371 79 255 1.265 .96 100 2210 6580 69 79 148 158 0 2367 101 2266 1.529 2345 2244 .654 1.393 .613 .478 .478
8 660 543 121 86 539 457 657 534 124 91 536 448 0 0 208 232 23 32 100 100 100 100 996 984 1.179 .848 .836 .817 .839 1.524 81 269 .884 .9 100 2360 6570 68 78 163 173 0 669 106 563 1.045 658 552 .957 1.03 .063 .043 .043
9 409 186 121 81 288 105 405 169 122 84 284 88 0 0 96 81 25 31 100 89 98 72 393 372 2.743 .365 .31 .323 .323 1.956 93 208 .4 .72 100 2510 6580 69 79 178 188 0 229 100 129 .449 208 108 2.226 .382 -1.154 -1.389 -1.389
10 2586 416 117 89 2469 327 2734 413 119 92 2617 324 0 0 707 148 23 29 100 99 100 97 2796 2941 7.55 .132 .124 .123 .129 1.566 118 308 .133 .92 120 2650 6570 67 79 191 203 0 513 110 403 .163 509 399 6.127 .153 -2.615 -2.713 -2.713
11 5139 365 115 89 5024 276 5667 354 118 93 5552 265 0 0 1483 162 23 34 100 95 100 93 5300 5817 18.203 .055 .048 .048 .054 1.887 94 234 .055 .86 110 2800 6580 68 79 206 217 0 450 110 340 .068 436 327 14.772 .059 -3.885 -4.088 -4.088
12 3311 7650 118 81 3193 7569 3359 7378 120 83 3241 7297 0 0 1538 3657 24 30 100 100 100 100 10762 10538 .422 2.37 2.251 2.441 2.372 1.473 86 233 2.42 .97 100 2950 6570 68 78 222 232 0 9427 100 9327 2.921 9092 8992 .342 2.774 1.546 1.472 1.472
13 3418 4956 118 83 3300 4873 3519 5136 120 88 3401 5053 0 0 1169 1543 23 30 100 100 100 100 8173 8454 .677 1.477 1.486 1.546 1.485 1.546 104 256 1.466 .96 110 3090 6570 67 78 235 246 0 6107 102 6005 1.82 6329 6227 .55 1.831 .864 .872 .872
14 379 213 116 85 263 128 374 211 118 90 258 126 0 0 73 58 22 31 100 96 100 91 391 384 2.055 .487 .488 .44 .467 1.829 89 264 .494 .82 110 3240 6570 67 78 250 261 0 262 105 158 .6 260 155 1.667 .602 -.738 -.733 -.733
15 964 171 115 83 849 88 1007 174 116 87 892 91 0 0 248 47 21 29 100 92 100 69 937 983 9.648 .104 .102 .095 .105 2.24 75 235 .089 .7 100 3390 6570 68 78 266 276 0 211 102 108 .128 214 112 7.829 .126 -2.969 -2.992 -2.992
16 2929 3415 119 89 2810 3326 3073 3550 120 92 2954 3461 0 0 1087 999 23 27 100 100 100 100 6136 6415 .845 1.184 1.172 1.282 1.167 1.613 93 263 1.139 .96 110 3540 6570 67 78 280 291 0 4208 110 4098 1.459 4374 4265 .686 1.444 .545 .53 .53
17 3025 4472 118 85 2907 4387 3349 4786 120 88 3231 4701 0 0 966 1653 24 28 100 100 100 100 7294 7932 .663 1.509 1.455 1.473 1.488 1.333 96 239 1.552 .97 110 3680 6570 67 78 294 305 0 5511 105 5406 1.86 5898 5793 .538 1.793 .895 .842 .842
18 1684 2725 118 85 1566 2640 1737 2926 120 90 1619 2841 0 0 481 633 23 32 100 100 100 100 4206 4460 .593 1.686 1.755 1.724 1.71 1.352 121 290 1.661 .96 120 3820 6570 67 79 308 320 0 3358 105 3253 2.077 3606 3501 .481 2.162 1.055 1.113 1.113
19 3579 3810 122 91 3457 3719 3739 3921 124 94 3617 3830 0 0 916 818 24 31 100 100 100 100 7176 7447 .93 1.076 1.059 1.109 1.08 1.436 131 286 1.053 .96 120 3970 6570 67 79 323 335 0 4695 112 4583 1.326 4832 4719 .754 1.305 .407 .384 .384
20 4001 4226 122 91 3879 4135 4362 4588 123 94 4240 4497 0 0 1359 1383 23 31 100 100 100 100 8014 8737 .938 1.066 1.061 1.103 1.034 1.509 109 341 1.058 .97 120 4120 6570 67 79 338 350 0 5207 112 5095 1.314 5654 5541 .761 1.307 .393 .386 .386

Total number of rows: 41472

Table truncated, full table size 9251 Kbytes.




Supplementary data files not provided
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