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Sample GSM93689 Query DataSets for GSM93689
Status Public on Jan 25, 2006
Title C8 vs R8
Sample type RNA
 
Channel 1
Source name C8
Organism Caenorhabditis elegans
Characteristics C8
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name R8
Organism Caenorhabditis elegans
Characteristics R8
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53247.gif
Measurement: concentration(absolute) 1000 uM
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 24, 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 GPL3391
Series (2)
GSE4094 N2 worms treated with Resveratrol
GSE4402 A role for SIR-2.1 regulation of ER stress response genes in determining C. elegans life span

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 10053 8882 156 180 9897 8702 11005 9532 167 190 10849 9352 0 0 3112 2806 59 73 100 100 100 100 18599 20201 1.137 .879 .862 .873 .867 1.259 120 397 .88 .98 120 2150 5800 25 37 55 67 0 9032 183 8849 .894 9693 9510 1.118 .877 -.162 -.19
2 790 462 156 183 634 279 805 462 167 193 649 279 0 0 200 126 53 71 98 95 98 89 913 928 2.272 .44 .43 .426 .42 1.6 120 427 .448 .83 120 2320 5800 25 37 72 84 0 470 186 284 .447 470 284 2.235 .437 -1.16 -1.194
3 505 392 157 180 348 212 486 381 163 184 329 201 0 0 112 105 39 53 100 97 100 82 560 530 1.642 .609 .611 .564 .583 1.83 120 410 .638 .73 120 2500 5800 25 37 90 102 0 399 183 216 .619 387 204 1.614 .621 -.691 -.687
4 514 760 157 178 357 582 514 771 161 183 357 593 0 0 125 193 42 54 98 99 97 97 939 950 .613 1.63 1.661 1.618 1.658 1.508 120 395 1.715 .89 120 2660 5800 25 37 106 118 0 773 181 592 1.658 784 603 .603 1.689 .729 .756
5 3410 2206 159 178 3251 2028 3458 2233 174 192 3299 2055 0 0 635 397 110 88 100 100 100 100 5279 5354 1.603 .624 .623 .623 .627 1.205 120 428 .614 .97 130 2830 5800 24 37 122 135 0 2243 181 2062 .634 2271 2090 1.576 .633 -.657 -.659
6 7749 7613 147 170 7602 7443 7668 7792 185 215 7521 7622 0 0 2114 2228 208 227 100 100 100 99 15045 15143 1.021 .979 1.013 .963 .987 1.219 120 483 .986 .98 130 3000 5800 24 37 139 152 0 7741 173 7568 .996 7923 7751 1.004 1.031 -.006 .043
7 155 130 124 154 31 -24 148 125 130 155 24 -29 0 0 66 45 32 45 38 7 11 3 7 -5 null null null 1.03 .917 4.464 80 400 4.656 .16 100 3180 5790 25 35 159 169 -50 132 157 -24 null 127 -29 null null null null
8 389 213 124 145 265 68 380 218 128 149 256 73 0 0 92 53 32 43 100 66 100 35 333 329 3.897 .257 .285 .224 .288 2.279 80 417 .505 .63 110 3340 5800 25 36 174 185 0 217 147 69 .261 222 74 3.832 .29 -1.938 -1.786
9 767 528 123 144 644 384 755 527 128 150 632 383 0 0 163 108 41 47 100 100 100 100 1028 1015 1.677 .596 .606 .591 .631 1.356 80 409 .618 .89 110 3500 5790 24 35 190 201 0 537 146 390 .606 536 389 1.649 .616 -.722 -.698
10 1370 777 120 146 1250 631 1355 763 132 155 1235 617 0 0 231 151 63 59 100 100 100 100 1881 1852 1.981 .505 .5 .497 .507 1.293 80 440 .493 .93 110 3670 5790 24 35 207 218 0 790 148 642 .513 776 627 1.948 .508 -.962 -.977
11 2409 1721 119 150 2290 1571 2433 1701 130 161 2314 1551 0 0 291 238 70 83 100 100 100 100 3861 3865 1.458 .686 .67 .683 .71 1.183 80 444 .687 .97 110 3840 5790 24 35 224 235 0 1750 153 1597 .698 1730 1577 1.434 .682 -.52 -.553
12 477 349 119 149 358 200 471 339 127 158 352 190 0 0 103 75 59 77 100 96 100 72 558 542 1.79 .559 .54 .538 .568 1.667 80 457 .562 .8 110 4010 5790 24 35 241 252 0 355 152 203 .568 345 193 1.76 .549 -.816 -.865
13 762 816 120 151 642 665 748 786 125 155 628 635 0 0 211 243 30 43 100 100 100 100 1307 1263 .965 1.036 1.011 1.035 1.01 1.361 80 462 1.047 .92 110 4190 5800 25 36 259 270 0 830 154 676 1.053 799 646 .949 1.028 .075 .04
14 198 185 124 156 74 29 171 171 127 158 47 15 0 0 85 74 31 40 68 36 38 16 103 62 2.552 .392 .319 .751 .865 3.195 80 372 .785 .45 100 4360 5790 25 35 277 287 -50 188 159 29 .398 174 15 2.509 .325 -1.327 -1.624
15 1070 1376 126 158 944 1218 1088 1394 128 160 962 1236 0 0 318 370 30 41 98 100 98 99 2162 2198 .775 1.29 1.285 1.344 1.298 1.565 120 420 1.287 .95 120 4520 5790 24 36 292 304 0 1399 161 1239 1.312 1418 1257 .762 1.306 .392 .386
16 289 268 128 162 161 106 282 257 133 167 154 95 0 0 85 83 43 57 93 69 79 37 267 249 1.519 .658 .617 .62 .684 2.528 120 436 .764 .64 120 4700 5790 24 36 310 322 0 273 165 108 .669 261 97 1.494 .627 -.579 -.673
17 697 887 132 162 565 725 699 867 138 170 567 705 0 0 165 197 49 65 100 100 100 100 1290 1272 .779 1.283 1.243 1.291 1.292 1.372 52 282 1.304 .92 90 4860 5810 27 36 327 336 0 902 165 737 1.305 882 717 .766 1.264 .384 .338
18 407 405 134 168 273 237 406 406 138 172 272 238 0 0 100 98 36 49 100 98 98 93 510 510 1.152 .868 .875 .865 .905 1.594 80 424 .923 .81 100 5020 5790 25 35 343 353 0 412 171 241 .883 413 242 1.133 .89 -.18 -.169
19 157 151 136 169 21 -18 150 144 143 178 14 -25 0 0 47 50 58 56 18 6 3 2 3 -11 null null null 1.583 1.513 3.272 80 374 5.294 .13 100 5210 5780 24 34 362 372 -50 154 172 -18 null 146 -25 null null null null
20 3813 5219 137 174 3676 5045 3900 5376 152 190 3763 5202 0 0 1063 1347 94 107 100 100 100 100 8721 8965 .729 1.372 1.382 1.39 1.393 1.194 120 438 1.366 .98 130 5370 5800 24 37 376 389 0 5307 177 5130 1.396 5467 5290 .717 1.406 .481 .491

Total number of rows: 20736

Table truncated, full table size 4494 Kbytes.




Supplementary data files not provided
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