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Sample GSM90829 Query DataSets for GSM90829
Status Public on Jan 06, 2006
Title Cycle, t=68hr
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-68, adult liver
Organism Austrofundulus limnaeus
Characteristics CY-68, adult liver
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: temperature acclimation, cycling acclimation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31223.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 42918 54945 108 69 42810 54876 44108 56645 146 110 44000 56576 0 6 6200 8909 473 461 100 100 100 100 97686 100576 .78 1.282 1.286 1 1 1 120 888 1 1 130 2030 26190 164 177 106 119 0 56644 71 56573 1.321 58397 58326 .757 1.326 .402 .407
2 28300 15510 111 69 28189 15441 30320 16649 146 106 30209 16580 0 0 5229 3171 457 444 100 100 100 100 43630 46789 1.826 .548 .549 1 1 1 156 951 1 1 140 2280 26200 165 179 131 145 0 15990 71 15919 .565 17164 17093 1.771 .566 -.824 -.822
3 26445 29666 110 67 26335 29599 29300 32996 113 70 29190 32929 0 0 6508 7402 19 18 100 100 100 100 55934 62119 .89 1.124 1.128 1 1 1 156 927 1 1 140 2520 26190 164 178 155 169 0 30584 69 30514 1.159 34016 33947 .863 1.163 .213 .218
4 2874 3068 102 62 2772 3006 2905 3154 107 65 2803 3092 0 0 510 490 25 18 100 100 100 100 5778 5895 .922 1.084 1.103 1 1 1 156 926 1 .99 140 2760 26190 164 178 179 193 0 3163 64 3099 1.118 3252 3188 .894 1.137 .161 .186
5 3842 3815 97 58 3745 3757 4042 4005 100 59 3945 3947 0 0 678 731 23 14 100 100 100 100 7502 7892 .997 1.003 1.001 1 1 1 156 926 1 1 140 3000 26190 164 178 203 217 0 3933 60 3873 1.034 4129 4069 .967 1.031 .049 .045
6 19335 24992 98 60 19237 24932 20344 26397 101 62 20246 26337 0 0 3371 4528 23 15 100 100 100 100 44169 46583 .772 1.296 1.301 1 1 1 156 942 1 1 140 3240 26190 164 178 227 241 0 25765 62 25703 1.336 27213 27152 .748 1.341 .418 .423
7 27908 31269 100 62 27808 31207 30061 34024 103 64 29961 33962 0 0 5725 6689 19 16 100 100 100 100 59015 63923 .891 1.122 1.134 1 1 1 156 928 1 1 140 3490 26190 164 178 252 266 0 32236 64 32172 1.157 35076 35012 .864 1.169 .21 .225
8 3029 3603 102 64 2927 3539 3057 3744 115 73 2955 3680 0 0 879 1015 65 44 100 100 100 100 6466 6635 .827 1.209 1.245 1 1 1 156 910 1 1 140 3720 26190 164 178 275 289 0 3714 66 3648 1.246 3860 3794 .802 1.284 .318 .36
9 885 753 97 60 788 693 876 718 105 66 779 658 0 0 205 212 49 35 100 100 100 100 1481 1437 1.137 .879 .845 1 1 1 156 1021 1 .99 150 3970 26190 163 178 299 314 0 776 62 714 .907 740 678 1.103 .871 -.141 -.2
10 19979 28652 104 66 19875 28586 20953 30041 111 73 20849 29975 0 0 3904 6310 54 43 100 100 100 100 48461 50824 .695 1.438 1.438 1 1 1 156 920 1 1 140 4200 26190 164 178 323 337 0 29538 68 29470 1.483 30970 30902 .674 1.482 .568 .568
11 3890 3704 104 65 3786 3639 4154 4034 108 70 4050 3969 0 0 896 958 34 31 100 100 100 100 7425 8019 1.04 .961 .98 1 1 1 156 1004 1 1 150 4440 26190 163 178 346 361 0 3819 67 3752 .991 4159 4092 1.009 1.01 -.013 .015
12 2698 2733 99 63 2599 2670 2608 2664 101 65 2509 2601 0 0 1244 1202 21 17 100 100 100 100 5269 5110 .973 1.027 1.037 1 1 1 156 936 1 .99 140 4680 26190 164 178 371 385 0 2818 65 2753 1.059 2746 2681 .944 1.069 .083 .096
13 4375 5628 97 60 4278 5568 4490 5779 98 62 4393 5719 0 0 708 1012 15 13 100 100 100 100 9846 10112 .768 1.302 1.302 1 1 1 156 939 1 1 140 4920 26190 164 178 395 409 0 5802 62 5740 1.342 5958 5896 .745 1.342 .424 .424
14 5012 5562 99 61 4913 5501 5404 6022 101 63 5305 5961 0 0 1055 1188 17 14 100 100 100 100 10414 11266 .893 1.12 1.124 1 1 1 156 929 1 1 140 5160 26180 163 177 419 433 0 5734 63 5671 1.154 6208 6145 .866 1.158 .207 .212
15 2719 2736 109 70 2610 2666 2855 2897 112 73 2746 2827 0 0 493 506 21 20 100 100 100 100 5276 5573 .979 1.021 1.029 1 1 1 156 927 1 .99 140 5400 26180 163 177 443 457 0 2821 72 2748 1.053 2987 2914 .95 1.061 .075 .086
16 3755 4952 118 76 3637 4876 3881 5170 121 79 3763 5094 0 0 632 898 21 19 100 100 100 100 8513 8857 .746 1.341 1.354 1 1 1 156 927 1 1 140 5640 26180 163 177 467 481 0 5105 78 5027 1.382 5330 5252 .724 1.396 .467 .481
17 9082 7701 114 73 8968 7628 9586 8166 121 79 9472 8093 0 0 1497 1373 68 64 100 100 100 100 16596 17565 1.176 .851 .854 1 1 1 156 927 1 1 140 5880 26180 163 177 491 505 0 7939 75 7864 .877 8419 8343 1.14 .881 -.19 -.183
18 18098 19989 100 65 17998 19924 18899 20822 107 71 18799 20757 0 0 2629 3036 67 63 100 100 100 100 37922 39556 .903 1.107 1.104 1 1 1 156 979 1 1 140 6120 26180 163 177 515 529 0 20607 67 20540 1.141 21466 21399 .876 1.138 .191 .187
19 42204 60000 106 68 42098 59932 44594 65223 130 90 44488 65155 0 43 7511 10355 381 342 100 100 100 100 102030 109643 .702 1.424 1.465 1 1 1 156 968 1 1 140 2040 26440 189 203 107 121 -100 61856 70 61786 1.468 67240 67170 .681 1.51 .554 .594
20 49068 61010 111 72 48957 60938 52243 65535 113 75 52132 65463 0 57 8515 9386 17 19 100 100 100 100 109895 117595 .803 1.245 1.256 1 1 1 156 854 1 1 140 2280 26430 188 202 131 145 -100 62897 74 62823 1.283 67562 67488 .779 1.295 .36 .372

Total number of rows: 4992

Table truncated, full table size 1117 Kbytes.




Supplementary data files not provided
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