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Sample GSM85970 Query DataSets for GSM85970
Status Public on Dec 03, 2005
Title 15MIN-2
Sample type RNA
 
Channel 1
Source name 13T (EtOH-treated) (green, channel 1)
Organism Caenorhabditis elegans
Characteristics 13T (EtOH-treated) (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 13C (N2) (red, channel 2)
Organism Caenorhabditis elegans
Characteristics 13C (N2) (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/12248.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 02, 2005
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 GPL2646
Series (1)
GSE3727 Ethanol-response genes and their regulation

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 6869 5648 834 836 6035 4812 null null 886 870 null null null null null null null null 95 97 null null null null 1.254 .797 null null .805 null 120 606 .778 .97 null null null 96 109 60 73 0 5088 753 4335 .718 null null 1.392 null -.477 null
2 2721 2635 732 807 1989 1828 null null 795 840 null null null null null null null null 87 94 null null null null 1.088 .919 null null .952 null 120 510 .796 .94 null null null 95 108 76 89 0 2373 727 1646 .828 null null 1.208 null -.273 null
3 1456 1501 788 836 668 665 null null 826 858 null null null null null null null null 66 71 null null null null 1.005 .996 null null 1.036 null 80 384 .701 .8 null null null 98 108 95 105 0 1352 753 599 .897 null null 1.115 null -.157 null
4 3772 3379 752 820 3020 2559 null null 772 844 null null null null null null null null 93 97 null null null null 1.18 .847 null null .88 null 80 388 .793 .96 null null null 98 109 111 122 0 3044 738 2306 .764 null null 1.31 null -.389 null
5 12436 12154 762 857 11674 11297 null null 784 896 null null null null null null null null 98 100 null null null null 1.033 .968 null null .968 null 80 411 .928 .97 null null null 98 109 127 138 0 10949 772 10177 .872 null null 1.147 null -.198 null
6 7655 5746 751 858 6904 4888 null null 774 894 null null null null null null null null 69 90 null null null null 1.412 .708 null null .787 null 52 280 .584 .92 null null null 97 106 145 154 0 5176 772 4404 .638 null null 1.568 null -.649 null
7 3397 3713 706 825 2691 2888 null null 731 861 null null null null null null null null 76 82 null null null null .932 1.073 null null 1.197 null 156 580 .863 .91 null null null 97 111 157 171 0 3345 743 2602 .967 null null 1.034 null -.049 null
8 9055 6482 700 847 8355 5635 null null 719 891 null null null null null null null null 85 90 null null null null 1.483 .674 null null .69 null 120 419 .595 .95 null null null 96 109 174 187 0 5839 763 5076 .608 null null 1.646 null -.719 null
9 19056 21462 840 960 18216 20502 null null 877 1019 null null null null null null null null 99 99 null null null null .888 1.125 null null 1.141 null 156 504 1.124 .98 null null null 96 110 190 204 0 19335 864 18471 1.014 null null .986 null .02 null
10 5973 4844 962 1068 5011 3776 null null 1013 1107 null null null null null null null null 96 97 null null null null 1.327 .754 null null .828 null 120 371 .67 .94 null null null 98 111 205 218 0 4363 962 3401 .679 null null 1.473 null -.559 null
11 8454 5789 722 890 7732 4899 null null 786 935 null null null null null null null null 95 93 null null null null 1.578 .634 null null .62 null 156 502 .617 .96 null null null 97 111 222 236 0 5215 801 4414 .571 null null 1.752 null -.809 null
12 2276 2210 581 825 1695 1385 null null 625 861 null null null null null null null null 89 85 null null null null 1.224 .817 null null .87 null 120 452 .583 .86 null null null 96 109 239 252 0 1990 743 1247 .736 null null 1.359 null -.443 null
13 8306 7793 543 780 7763 7013 null null 550 811 null null null null null null null null 98 90 null null null null 1.107 .903 null null .919 null 80 358 .883 .97 null null null 99 110 255 266 0 7020 702 6318 .814 null null 1.229 null -.297 null
14 1190 1425 486 704 704 721 null null 494 716 null null null null null null null null 87 91 null null null null .976 1.024 null null .989 null 80 410 .81 .85 null null null 99 110 271 282 0 1283 634 649 .922 null null 1.085 null -.117 null
15 840 1210 459 684 381 526 null null 465 702 null null null null null null null null 70 79 null null null null .724 1.381 null null 1.394 null 120 441 .981 .83 null null null 99 111 287 299 0 1090 616 474 1.244 null null .804 null .315 null
16 1822 2143 429 682 1393 1461 null null 441 710 null null null null null null null null 73 80 null null null null .953 1.049 null null 1.09 null 156 515 .886 .9 null null null 98 112 303 317 0 1930 614 1316 .945 null null 1.059 null -.082 null
17 5546 5311 422 691 5124 4620 null null 431 716 null null null null null null null null 80 77 null null null null 1.109 .902 null null .921 null 120 371 .859 .96 null null null 99 111 320 332 0 4784 622 4162 .812 null null 1.231 null -.3 null
18 1434 1863 415 686 1019 1177 null null 423 714 null null null null null null null null 84 84 null null null null .866 1.155 null null 1.142 null 120 352 1.028 .93 null null null 99 111 336 348 0 1678 618 1060 1.04 null null .961 null .057 null
19 3743 4206 400 700 3343 3506 null null 413 726 null null null null null null null null 83 90 null null null null .954 1.049 null null 1.083 null 156 479 .926 .95 null null null 97 111 350 364 0 3789 630 3159 .945 null null 1.058 null -.082 null
20 5130 5947 382 724 4748 5223 null null 393 744 null null null null null null null null 91 95 null null null null .909 1.1 null null 1.092 null 156 484 1.034 .96 null null null 97 111 367 381 0 5357 652 4705 .991 null null 1.009 null -.013 null

Total number of rows: 21504

Table truncated, full table size 5235 Kbytes.




Supplementary data files not provided
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