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Sample GSM90822 Query DataSets for GSM90822
Status Public on Jan 06, 2006
Title Cycle, t=12hr
Sample type RNA
 
Channel 1
Source name Liver Reference RNA 4/17/02 (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics Liver Reference RNA 4/17/02 (pooled, 1 ug poly-A)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CY-12, adult liver (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics CY-12, adult liver (pooled, 1 ug poly-A)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: temperature acclimation, cycling acclimation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31115.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 05, 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 GPL3311
Series (1)
GSE3981 Temperature acclimation

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 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
1 29229 49368 70 65 29159 49303 29849 50478 80 128 29779 50413 0 0 5085 10499 127 702 100 100 100 100 78462 80192 .591 1.691 1.693 1 1 1 120 862 1 .98 130 2140 26310 140 153 117 130 0 34766 46 34720 1.191 35548 35502 .84 1.192 .252 .254
2 12997 14118 71 67 12926 14051 13173 14516 87 123 13102 14449 0 0 936 1571 178 542 100 100 100 100 26977 27551 .92 1.087 1.103 1 1 1 120 850 1 .99 130 2380 26310 140 153 141 154 0 9942 47 9895 .766 10223 10175 1.306 .777 -.385 -.365
3 9779 17189 70 66 9709 17123 9105 15063 79 85 9035 14997 0 0 4465 8443 123 256 100 100 100 100 26832 24032 .567 1.764 1.66 1 1 1 156 970 1 .99 140 2630 26310 140 154 166 180 0 12105 46 12058 1.242 10608 10561 .805 1.169 .313 .225
4 970 1439 70 65 900 1374 957 1460 72 71 887 1395 0 0 140 279 18 44 100 100 100 100 2274 2282 .655 1.527 1.573 1 1 1 120 824 1 .98 130 2860 26300 139 152 189 202 0 1013 46 968 1.075 1028 982 .93 1.108 .104 .147
5 1867 3061 69 65 1798 2996 2021 3219 71 69 1952 3154 0 0 470 726 16 36 99 100 99 100 4794 5106 .6 1.666 1.616 1 1 1 156 951 1 .99 140 3110 26310 140 154 214 228 0 2156 46 2110 1.173 2267 2221 .852 1.138 .231 .186
6 8469 11289 71 64 8398 11225 8796 11350 71 66 8725 11286 0 0 2414 3405 8 21 100 100 100 100 19623 20011 .748 1.337 1.294 1 1 1 156 921 1 .99 140 3350 26310 140 154 238 252 0 7950 45 7905 .941 7993 7948 1.062 .911 -.087 -.135
7 14971 27455 71 66 14900 27389 16236 29683 72 68 16165 29617 0 0 3593 6201 9 18 100 100 100 100 42289 45782 .544 1.838 1.832 1 1 1 156 921 1 .99 140 3590 26310 140 154 262 276 0 19335 46 19288 1.294 20904 20857 .772 1.29 .372 .368
8 1120 1375 70 64 1050 1311 1110 1317 71 65 1040 1253 0 0 341 460 8 17 100 100 99 100 2361 2293 .801 1.249 1.205 1 1 1 156 921 1 .98 140 3830 26310 140 154 286 300 0 968 45 923 .879 927 882 1.137 .848 -.186 -.237
9 420 498 70 66 350 432 428 492 92 96 358 426 0 0 106 163 150 217 95 92 69 47 782 784 .81 1.234 1.19 1 1 1 156 921 1 .95 140 4070 26310 140 154 310 324 0 351 46 304 .869 346 300 1.15 .838 -.202 -.255
10 6812 11025 71 69 6741 10956 7013 11055 98 107 6942 10986 0 0 1961 3371 176 253 99 99 99 99 17697 17928 .615 1.625 1.583 1 1 1 156 920 1 .99 140 4310 26310 140 154 334 348 0 7764 49 7715 1.145 7785 7737 .874 1.114 .195 .156
11 1756 2491 69 63 1687 2428 1923 2630 70 65 1854 2567 0 0 433 653 8 17 100 100 100 100 4115 4421 .695 1.439 1.385 1 1 1 156 923 1 .99 140 4550 26310 140 154 358 372 0 1754 44 1710 1.014 1852 1808 .987 .975 .019 -.036
12 1161 2106 68 62 1093 2044 1220 2161 69 64 1152 2099 0 0 322 610 9 16 99 100 99 100 3137 3251 .535 1.87 1.822 1 1 1 156 923 1 .98 140 4790 26310 140 154 382 396 0 1483 44 1439 1.317 1522 1478 .759 1.283 .397 .36
13 2109 4100 68 64 2041 4036 2199 4183 70 67 2131 4119 0 0 496 906 12 20 99 100 99 100 6077 6250 .506 1.977 1.933 1 1 1 156 940 1 .98 140 5030 26310 140 154 406 420 0 2887 45 2842 1.393 2946 2901 .718 1.361 .478 .445
14 2266 4141 69 65 2197 4076 2417 4382 71 68 2348 4317 0 0 441 872 18 23 100 100 100 100 6273 6665 .539 1.855 1.839 1 1 1 156 922 1 .99 140 5270 26300 139 153 430 444 0 2916 46 2870 1.307 3086 3040 .765 1.295 .386 .373
15 1362 2333 70 65 1292 2268 1410 2425 72 68 1340 2360 0 0 291 547 17 21 100 100 100 100 3560 3700 .57 1.755 1.761 1 1 1 156 988 1 .98 150 5500 26300 138 153 452 467 0 1643 46 1597 1.236 1708 1662 .809 1.24 .306 .311
16 1725 2144 71 65 1654 2079 1885 2295 72 68 1814 2230 0 0 412 530 10 18 100 100 100 100 3733 4044 .796 1.257 1.229 1 1 1 156 921 1 .99 140 5740 26300 139 153 477 491 0 1510 46 1464 .885 1616 1570 1.13 .866 -.176 -.208
17 3905 5859 70 64 3835 5795 4121 6094 71 67 4051 6030 0 0 763 1114 9 19 100 100 100 100 9630 10081 .662 1.511 1.489 1 1 1 156 938 1 .99 140 5980 26300 139 153 501 515 0 4126 45 4081 1.064 4292 4246 .94 1.048 .09 .068
18 7825 18048 69 67 7756 17981 8392 19261 71 69 8323 19194 0 0 1452 3261 10 21 100 100 100 100 25737 27517 .431 2.318 2.306 1 1 1 156 988 1 .99 140 6220 26300 139 153 525 539 0 12710 47 12663 1.633 13564 13517 .613 1.624 .707 .7
19 29169 51068 71 67 29098 51001 31402 54168 79 125 31331 54101 0 5 7793 14987 120 673 100 100 99 100 80099 85432 .571 1.753 1.727 1 1 1 156 939 1 .99 140 2140 26540 163 177 117 131 0 35963 47 35916 1.234 38146 38099 .81 1.216 .304 .282
20 31979 55477 73 72 31906 55405 35370 61966 80 99 35297 61894 0 39 9879 14680 110 306 98 100 98 99 87311 97191 .576 1.737 1.754 1 1 1 156 869 1 .99 140 2380 26550 164 178 141 155 -100 39068 51 39018 1.223 43638 43587 .818 1.235 .29 .304

Total number of rows: 4992

Table truncated, full table size 1094 Kbytes.




Supplementary data files not provided
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