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Sample GSM95251 Query DataSets for GSM95251
Status Public on Feb 03, 2006
Title N2 (green, channel 1) vs daf-14 (red, channel 2) Trial #3
Sample type RNA
 
Channel 1
Source name N2 (green, channel 1)
Organism Caenorhabditis elegans
Characteristics N2 (green, channel 1)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name daf-14 (red, channel 2)
Organism Caenorhabditis elegans
Characteristics daf-14 (red, channel 2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: dauer, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15551.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 Feb 02, 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 GPL2754
Series (1)
GSE4164 Regulation of signaling genes by TGFbeta during entry into dauer diapause in C. elegans

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
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 11520 11738 92 150 11428 11588 16022 12218 95 153 15930 12068 0 0 7535 9144 28 42 100 100 100 100 23016 27998 .986 1.014 .758 .835 .889 2.437 80 516 1.097 .95 110 2130 18340 40 51 47 58 0 10736 137 10599 .927 11175 11038 1.078 .693 -.109 -.529
2 2983 2125 92 157 2891 1968 3157 2056 94 161 3065 1899 0 0 702 725 28 43 100 100 100 100 4859 4964 1.469 .681 .62 .666 .647 1.366 52 292 .685 .92 80 2290 18330 41 49 65 73 0 1944 144 1800 .623 1881 1737 1.606 .567 -.684 -.819
3 313 265 87 150 226 115 316 255 89 156 229 105 0 0 71 75 23 41 100 82 98 63 341 334 1.965 .509 .459 .425 .474 2.214 52 307 .534 .67 80 2460 18330 41 49 82 90 0 242 137 105 .465 233 96 2.149 .419 -1.103 -1.254
4 3427 2106 95 160 3332 1946 3836 2178 99 168 3741 2018 0 0 985 853 29 57 100 100 100 100 5278 5759 1.712 .584 .539 .567 .56 1.57 52 313 .594 .93 80 2630 18330 41 49 99 107 0 1926 146 1780 .534 1992 1846 1.872 .493 -.905 -1.019
5 15831 26421 107 172 15724 26249 17069 27087 115 178 16962 26915 0 0 3484 10910 49 56 100 100 100 100 41973 43877 .599 1.669 1.587 1.53 1.594 1.568 52 374 1.825 .94 90 2790 18340 41 50 114 123 0 24166 157 24008 1.527 24775 24618 .655 1.451 .611 .537
6 1268 1402 110 161 1158 1241 1237 1451 116 161 1127 1290 0 0 592 485 43 39 100 100 100 100 2399 2417 .933 1.072 1.145 1.153 1.033 1.383 12 98 .961 .93 50 2950 18320 41 46 132 137 0 1282 147 1135 .98 1327 1180 1.02 1.047 -.029 .066
7 13329 27815 110 182 13219 27633 14940 30070 114 189 14830 29888 0 0 4330 11202 33 54 100 100 100 100 40852 44718 .478 2.09 2.015 2.013 2.067 1.407 80 519 2.213 .96 110 3100 18340 40 51 144 155 0 25441 166 25274 1.912 27503 27337 .523 1.843 .935 .882
8 644 892 116 194 528 698 671 931 119 200 555 737 0 0 182 219 34 57 98 100 98 98 1226 1292 .756 1.322 1.328 1.383 1.289 1.778 52 354 1.354 .92 90 3270 18340 41 50 162 171 0 816 177 638 1.209 852 674 .827 1.215 .274 .28
9 849 545 107 187 742 358 849 544 112 190 742 357 0 0 143 116 39 46 100 100 100 98 1100 1099 2.073 .482 .481 .465 .476 1.371 52 365 .437 .87 90 3430 18340 41 50 178 187 0 498 171 327 .441 498 327 2.266 .44 -1.18 -1.184
10 574 651 96 176 478 475 598 687 103 180 502 511 0 0 124 135 42 46 100 100 98 100 953 1013 1.006 .994 1.018 1.011 1.008 1.502 52 334 .986 .89 90 3590 18340 41 50 194 203 0 595 161 434 .909 628 467 1.1 .931 -.138 -.103
11 15593 11140 101 183 15492 10957 17808 12445 115 191 17707 12262 0 0 5435 3709 63 72 100 100 100 100 26449 29969 1.414 .707 .692 .722 .705 1.496 52 360 .689 .97 90 3740 18340 41 50 209 218 0 10189 167 10022 .647 11383 11215 1.546 .633 -.628 -.659
12 664 529 111 196 553 333 676 534 121 202 565 338 0 0 142 133 62 64 100 100 98 92 886 903 1.661 .602 .598 .575 .62 1.648 52 303 .595 .86 80 3920 18340 42 50 228 236 0 484 179 305 .551 488 309 1.816 .547 -.86 -.87
13 245 273 96 175 149 98 151 231 100 181 55 56 0 0 378 155 31 47 65 53 46 32 247 111 1.52 .658 1.018 1.009 1.17 4.041 52 294 .405 .78 80 4060 18330 41 49 242 250 -50 250 160 90 .602 211 51 1.662 .931 -.733 -.103
14 317 335 96 184 221 151 320 335 101 189 224 151 0 0 71 84 31 43 100 90 100 76 372 375 1.464 .683 .674 .631 .689 1.727 52 314 .776 .73 80 4230 18340 42 50 259 267 0 306 168 138 .625 306 138 1.6 .617 -.678 -.698
15 673 568 116 214 557 354 674 573 129 231 558 359 0 0 126 115 59 79 100 100 98 98 911 917 1.573 .636 .643 .621 .65 1.501 52 294 .595 .82 80 4400 18340 42 50 276 284 0 520 196 324 .581 524 328 1.72 .588 -.783 -.765
16 662 813 192 397 470 416 681 795 249 556 489 398 0 0 188 183 161 407 94 42 82 1 886 887 1.13 .885 .814 .883 .866 1.563 52 288 1.194 .7 80 4540 18340 42 50 290 298 -50 744 363 380 .81 727 364 1.235 .744 -.305 -.426
17 12217 3967 134 261 12083 3706 14030 3999 213 468 13896 3738 0 0 5946 1918 173 446 100 91 100 88 15789 17634 3.26 .307 .269 .31 .305 1.837 80 454 .293 .95 100 4720 18340 41 51 307 317 0 3628 239 3390 .281 3658 3419 3.565 .246 -1.834 -2.023
18 543 455 102 190 441 265 526 445 106 196 424 255 0 0 114 76 30 48 100 100 100 98 706 679 1.664 .601 .601 .608 .582 1.441 52 282 .583 .84 80 4880 18340 42 50 324 332 0 416 174 242 .55 407 233 1.819 .55 -.864 -.862
19 3843 4998 101 190 3742 4808 4252 5299 107 195 4151 5109 0 0 1661 2278 33 47 100 100 100 100 8550 9260 .778 1.285 1.231 1.306 1.269 1.737 80 432 1.317 .96 100 5040 18340 41 51 339 349 0 4571 174 4398 1.175 4847 4673 .851 1.126 .233 .171
20 1496 596 111 196 1385 400 1519 593 116 199 1408 397 0 0 224 192 32 46 100 98 100 94 1785 1805 3.463 .289 .282 .249 .263 1.829 52 332 .283 .86 90 5210 18350 42 51 356 365 0 545 179 366 .264 542 363 3.786 .258 -1.921 -1.955

Total number of rows: 21504

Table truncated, full table size 4752 Kbytes.




Supplementary data files not provided

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