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Sample GSM93687 Query DataSets for GSM93687
Status Public on Jan 25, 2006
Title dCf-16 C
Sample type RNA
 
Channel 1
Source name CC
Organism Caenorhabditis elegans
Characteristics CC
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name RC
Organism Caenorhabditis elegans
Characteristics RC
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs//54806.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)
GSE4093 Resveratrol treatment of daf-16 mutant C. elegans
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 4637 3245 101 72 4536 3173 4666 3225 124 94 4565 3153 0 0 778 845 104 87 100 100 100 100 7709 7718 1.43 .7 .691 .671 .711 1.39 120 430 .719 .95 130 1640 5500 27 40 61 74 0 4136 92 4045 .892 4111 4019 1.121 .88 -.165 -.184
2 398 227 102 69 296 158 401 222 122 88 299 153 0 0 83 84 102 81 99 82 86 45 454 452 1.873 .534 .512 .491 .532 1.981 120 426 .569 .73 130 1830 5500 27 40 80 93 0 289 88 201 .68 283 195 1.47 .652 -.556 -.616
3 330 175 96 64 234 111 330 164 99 68 234 100 0 0 91 67 29 29 100 88 97 76 345 334 2.108 .474 .427 .418 .437 2.305 120 361 .439 .65 120 2000 5500 28 40 98 110 0 223 82 141 .605 209 127 1.654 .545 -.726 -.876
4 272 177 95 64 177 113 260 155 96 69 165 91 0 0 71 82 27 33 100 85 98 64 290 256 1.566 .638 .552 .565 .665 2.59 120 378 .701 .58 120 2170 5500 28 40 115 127 0 226 82 144 .814 198 116 1.229 .703 -.297 -.508
5 868 667 98 70 770 597 924 678 119 91 826 608 0 0 315 233 93 87 93 97 92 94 1367 1434 1.29 .775 .736 .842 .756 1.94 156 439 .754 .91 140 2340 5510 28 42 131 145 0 850 89 761 .988 864 775 1.012 .938 -.017 -.092
6 5304 3441 102 73 5202 3368 5123 3499 143 116 5021 3426 0 0 923 773 136 134 100 100 100 99 8570 8447 1.545 .647 .682 .632 .655 1.364 120 383 .664 .93 130 2500 5500 27 40 147 160 0 4386 93 4293 .825 4460 4367 1.212 .87 -.277 -.201
7 198 99 99 67 99 32 198 92 108 80 99 25 0 0 47 40 63 58 72 21 25 3 131 124 3.094 .323 .253 .34 .351 2.737 80 397 .362 .29 110 2670 5500 28 39 165 176 0 126 85 41 .412 117 32 2.427 .322 -1.279 -1.635
8 253 140 103 72 150 68 250 137 108 78 147 65 0 0 62 57 38 39 97 67 87 40 218 212 2.206 .453 .442 .439 .473 2.315 80 374 .443 .41 110 2850 5510 29 40 183 194 0 178 92 87 .578 175 83 1.731 .564 -.791 -.827
9 595 487 106 73 489 414 602 491 114 81 496 418 0 0 122 130 42 43 100 100 100 100 903 914 1.181 .847 .843 .827 .823 1.532 120 417 .858 .86 130 2990 5500 27 40 196 209 0 621 93 528 1.079 626 533 .927 1.074 .11 .103
10 260 180 105 73 155 107 249 172 112 80 144 99 0 0 77 79 40 43 96 75 83 61 262 243 1.449 .69 .688 .606 .623 3.424 80 391 .672 .48 110 3170 5490 27 38 215 226 0 229 93 136 .88 219 126 1.136 .876 -.184 -.19
11 1153 734 113 80 1040 654 1124 729 132 95 1011 649 0 0 216 180 80 71 100 100 100 99 1694 1660 1.59 .629 .642 .615 .636 1.435 120 412 .622 .89 130 3350 5500 27 40 232 245 0 936 102 834 .802 929 827 1.248 .818 -.319 -.289
12 577 381 110 78 467 303 574 365 125 90 464 287 0 0 147 132 73 66 99 100 99 91 770 751 1.541 .649 .619 .622 .623 1.797 120 360 .627 .8 120 3500 5500 28 40 248 260 0 486 99 386 .827 465 366 1.209 .788 -.274 -.343
13 744 1192 101 70 643 1122 727 1186 104 74 626 1116 0 0 215 388 32 33 100 100 100 100 1765 1742 .573 1.745 1.783 1.723 1.804 1.801 120 386 1.897 .87 120 3680 5500 28 40 266 278 0 1519 89 1430 2.224 1512 1423 .45 2.272 1.153 1.184
14 228 148 100 69 128 79 223 141 104 74 123 72 0 0 63 64 33 33 95 73 84 52 207 195 1.62 .617 .585 .57 .676 3.053 120 383 .598 .47 120 3860 5500 28 40 284 296 0 189 88 101 .787 180 92 1.271 .746 -.346 -.422
15 771 993 104 72 667 921 769 1041 110 83 665 969 0 0 196 233 45 51 100 100 99 100 1588 1634 .724 1.381 1.457 1.4 1.381 1.483 120 368 1.413 .9 130 4030 5500 27 40 300 313 0 1266 92 1174 1.76 1327 1235 .568 1.857 .816 .893
16 267 156 102 72 165 84 262 145 108 80 160 73 0 0 72 65 42 49 97 65 88 36 249 233 1.964 .509 .456 .468 .49 2.795 120 398 .481 .54 130 4190 5500 27 40 316 329 0 199 92 107 .649 185 93 1.541 .582 -.624 -.782
17 223 175 98 70 125 105 228 171 100 73 130 101 0 0 71 84 31 31 88 78 78 63 230 231 1.19 .84 .777 .815 .842 2.527 52 266 .874 .59 90 4370 5490 28 37 336 345 0 223 89 134 1.071 218 129 .934 .99 .099 -.014
18 400 273 95 66 305 207 405 268 100 72 310 202 0 0 113 97 31 32 100 96 96 94 512 512 1.473 .679 .652 .685 .654 1.735 156 424 .67 .81 140 4510 5500 27 41 348 362 0 348 84 264 .865 342 257 1.156 .831 -.209 -.268
19 199 110 97 70 102 40 199 105 107 90 102 35 0 0 46 47 88 163 61 0 5 0 142 137 2.55 .392 .343 .542 .567 3.09 80 360 .421 .39 110 4700 5490 27 38 368 379 0 140 89 51 .5 134 45 2 .437 -1 -1.193
20 6313 10626 101 78 6212 10548 6375 10720 154 177 6274 10642 0 0 1173 3051 198 363 100 100 100 98 16760 16916 .589 1.698 1.696 1.6 1.71 1.465 120 370 1.808 .97 130 4860 5490 26 39 383 396 0 13545 99 13446 2.164 13665 13565 .462 2.162 1.114 1.112

Total number of rows: 20736

Table truncated, full table size 4417 Kbytes.




Supplementary data files not provided
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