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Sample GSM90819 Query DataSets for GSM90819
Status Public on Jan 06, 2006
Title Cycle, t=8hr
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-8, adult liver (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics CY-8, 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/2002-07/31114.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 35141 44246 99 67 35042 44179 38680 47779 102 70 38581 47712 0 0 11073 15144 17 21 100 100 100 100 79221 86293 .793 1.261 1.237 1 1 1 156 973 1 1 140 2110 26040 113 127 114 128 0 40593 61 40531 1.157 43834 43772 .865 1.135 .21 .182
2 14076 26280 109 77 13967 26203 15786 29277 112 80 15677 29200 0 0 4470 8405 21 29 100 100 99 100 40170 44877 .533 1.876 1.863 1 1 1 156 922 1 1 140 2340 26040 113 127 137 151 0 24110 71 24039 1.721 26860 26789 .581 1.709 .783 .773
3 15979 28456 112 79 15867 28377 18159 32602 114 82 18047 32523 0 0 5342 10650 20 25 100 100 100 100 44244 50570 .559 1.788 1.802 1 1 1 156 938 1 .99 140 2590 26030 112 126 162 176 0 26106 72 26034 1.641 29910 29838 .609 1.653 .714 .725
4 1307 1571 109 75 1198 1496 1341 1593 111 78 1232 1518 0 0 306 436 23 24 100 100 100 100 2694 2750 .801 1.249 1.232 1 1 1 156 920 1 .99 140 2820 26030 112 126 185 199 0 1441 69 1372 1.146 1461 1393 .873 1.13 .196 .177
5 2508 2696 107 72 2401 2624 2651 2885 110 75 2544 2813 0 0 521 617 30 26 100 100 100 100 5025 5357 .915 1.093 1.106 1 1 1 156 938 1 .99 140 3070 26030 112 126 210 224 0 2473 66 2407 1.003 2647 2581 .997 1.014 .004 .021
6 10903 11473 104 70 10799 11403 11242 11518 108 73 11138 11448 0 0 2548 3116 28 23 100 100 100 100 22202 22586 .947 1.056 1.028 1 1 1 156 920 1 1 140 3300 26030 112 126 233 247 0 10526 64 10461 .969 10567 10503 1.032 .943 -.046 -.085
7 19497 30349 102 68 19395 30281 20953 32952 107 77 20851 32884 0 0 4490 7440 72 128 100 100 100 100 49676 53735 .641 1.561 1.577 1 1 1 156 971 1 1 140 3550 26030 112 126 258 272 0 27843 62 27781 1.432 30231 30169 .698 1.447 .518 .533
8 1659 1448 97 65 1562 1383 1635 1392 103 76 1538 1327 0 0 314 364 78 140 100 100 100 100 2945 2865 1.129 .885 .863 1 1 1 120 812 1 .98 130 3790 26020 111 124 282 295 0 1328 60 1269 .812 1277 1217 1.231 .792 -.3 -.337
9 555 501 94 61 461 440 573 478 97 64 479 417 0 0 138 180 36 24 100 100 100 100 901 896 1.048 .954 .871 1 1 1 156 922 1 .96 140 4020 26030 112 126 305 319 0 460 56 404 .876 439 383 1.142 .799 -.192 -.324
10 9652 11735 92 59 9560 11676 9888 11552 95 63 9796 11493 0 0 2941 3984 37 22 100 100 99 100 21236 21289 .819 1.221 1.173 1 1 1 156 922 1 .99 140 4260 26030 112 126 329 343 0 10766 54 10712 1.12 10598 10544 .892 1.076 .164 .106
11 2237 2530 91 59 2146 2471 2386 2625 94 62 2295 2566 0 0 487 622 21 18 100 100 100 100 4617 4861 .868 1.151 1.118 1 1 1 156 936 1 .99 140 4500 26030 112 126 353 367 0 2321 54 2267 1.056 2408 2354 .947 1.026 .079 .037
12 1693 1776 91 59 1602 1717 1668 1733 95 63 1577 1674 0 0 240 311 42 37 100 100 100 100 3319 3251 .933 1.072 1.062 1 1 1 120 838 1 .99 130 4740 26020 111 124 377 390 0 1629 54 1575 .983 1590 1536 1.017 .974 -.024 -.038
13 3213 3540 93 61 3120 3479 3262 3571 101 67 3169 3510 0 0 420 628 82 66 100 100 100 100 6599 6679 .897 1.115 1.108 1 1 1 120 850 1 .99 130 4980 26020 111 124 401 414 0 3248 56 3192 1.023 3276 3220 .978 1.016 .033 .023
14 3159 4217 94 62 3065 4155 3176 4187 102 69 3082 4125 0 0 248 473 84 71 100 100 100 100 7220 7207 .738 1.356 1.338 1 1 1 120 838 1 .99 130 5220 26020 111 124 425 438 0 3869 57 3812 1.244 3841 3784 .804 1.228 .315 .296
15 1993 2439 93 62 1900 2377 1989 2464 104 75 1896 2402 0 0 209 325 120 139 100 100 100 100 4277 4298 .799 1.251 1.267 1 1 1 120 858 1 .99 130 5450 26020 111 124 448 461 0 2238 57 2181 1.148 2261 2204 .871 1.162 .199 .217
16 2263 2514 93 62 2170 2452 2280 2540 99 69 2187 2478 0 0 304 415 66 80 100 100 100 100 4622 4665 .885 1.13 1.133 1 1 1 120 831 1 .99 130 5710 26020 111 124 474 487 0 2306 57 2250 1.037 2330 2273 .965 1.04 .052 .056
17 5135 6983 92 62 5043 6921 5551 7487 96 64 5459 7425 0 0 1471 2031 23 20 99 99 99 99 11964 12884 .729 1.372 1.36 1 1 1 156 922 1 .99 140 5940 26020 111 125 497 511 0 6406 57 6350 1.259 6869 6812 .794 1.248 .332 .319
18 9918 16698 91 63 9827 16635 10419 17768 96 66 10328 17705 0 0 2133 3637 25 20 100 100 100 100 26462 28033 .591 1.693 1.714 1 1 1 156 978 1 .99 140 6180 26020 111 125 521 535 0 15319 58 15261 1.553 16301 16243 .644 1.573 .635 .653
19 40517 48146 99 69 40418 48077 44945 51644 102 74 44846 51575 0 1 13401 16441 22 27 100 100 100 100 88495 96421 .841 1.189 1.15 1 1 1 156 921 1 1 140 2100 26270 136 150 113 127 0 44171 63 44107 1.091 47380 47317 .916 1.055 .126 .077
20 47833 62206 110 80 47723 62126 48647 65535 119 94 48537 65455 0 52 4569 4944 118 166 100 100 100 100 109849 113992 .768 1.302 1.349 1 1 1 120 770 1 1 130 2340 26260 135 148 137 150 0 57070 73 56996 1.194 60124 60050 .837 1.237 .256 .307

Total number of rows: 4992

Table truncated, full table size 1112 Kbytes.




Supplementary data files not provided
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