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Sample GSM306255 Query DataSets for GSM306255
Status Public on Jul 29, 2008
Title fer-15 (A) vs. N2 mixed stage ref
Sample type RNA
 
Channel 1
Source name N2 mixed stage ref
Organism Caenorhabditis elegans
Characteristics N2 mixed stage ref
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name fer-15
Organism Caenorhabditis elegans
Characteristics fer-15
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30518.gif
Place of growth: Stanford
Genotype: fer-15
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 Jul 18, 2008
Last update date Jul 29, 2008
Contact name Stuart Kim
E-mail(s) kim@cmgm.stanford.edu
Phone 650-725-7671
Fax 650-725-7739
Organization name Stanford University Medical Center
Department Department of Developmental Biology
Street address -
City Stanford
State/province CA
ZIP/Postal code 94305-5307
Country USA
 
Platform ID GPL7065
Series (3)
GSE12094 Aging study
GSE12166 TJ411(fer-15(b26)II; age-1(hx542)II) vs. BA713(fer-15(b26)II)
GSE12167 TJ1081)fer-15(b26)II; daf-16(m26)I) vs. BA713(fer-15(b26)II)

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 1377 818 138 246 1239 572 1347 745 147 248 1209 499 0 0 870 460 40 46 96 78 87 78 1811 1708 2.166 .462 .413 .469 .49 .154 32 230 .446 .93 70 2180 18590 84 91 109 116 0 1410 424 986 .796 1284 860 1.256 .712 -.329 -.491
2 1199 396 138 225 1061 171 1237 381 152 240 1099 156 0 0 321 87 113 94 100 76 100 40 1232 1255 6.205 .161 .142 .157 .156 .064 52 310 .178 .69 80 2340 18590 84 92 125 133 0 683 388 295 .278 657 269 3.599 .245 -1.847 -2.031
3 490 115 135 179 355 -64 477 110 141 185 342 -69 0 0 107 25 37 45 100 0 100 0 291 273 null null null 0 0 0 32 230 -.114 -.46 70 2500 18590 84 91 141 148 0 198 309 -110 null 190 null null null null null
4 1087 1858 129 183 958 1675 1104 2073 134 186 975 1890 0 0 258 526 35 42 100 100 100 100 2633 2865 .572 1.748 1.938 1.755 1.771 .425 32 230 1.689 .96 70 2670 18580 83 90 158 165 0 3203 316 2888 3.015 3574 3259 .332 3.342 1.592 1.741
5 872 267 129 175 743 92 881 262 134 177 752 87 0 0 160 41 36 35 100 92 100 67 835 839 8.076 .124 .116 .126 .125 .057 52 366 .125 .77 90 2820 18580 82 91 172 181 0 460 302 159 .213 452 150 4.684 .199 -2.228 -2.326
6 601 584 123 167 478 417 418 315 127 169 295 148 0 0 535 535 33 31 76 69 63 57 895 443 1.146 .872 .502 .904 .811 .481 52 305 .914 .96 80 2980 18570 82 90 189 197 0 1007 288 719 1.504 543 255 .665 .865 .589 -.209
7 2002 821 120 139 1882 682 2088 837 137 137 1968 698 0 0 454 142 98 34 100 100 100 100 2564 2666 2.76 .362 .355 .371 .359 .064 52 379 .349 .97 90 3140 18570 81 90 204 213 0 1416 240 1176 .625 1443 1203 1.601 .612 -.679 -.71
8 536 173 120 112 416 61 546 162 129 114 426 50 0 0 126 44 42 29 100 83 100 41 477 476 6.82 .147 .117 .169 .18 .106 12 104 .133 .58 50 3290 18580 84 89 221 226 0 298 193 105 .253 279 86 3.955 .202 -1.984 -2.305
9 1795 9440 122 137 1673 9303 1959 10540 127 138 1837 10403 0 0 593 2893 40 35 100 100 100 100 10976 12240 .18 5.561 5.663 5.994 5.62 2.639 80 462 5.357 .98 100 3480 18570 81 91 238 248 0 16276 236 16040 9.587 18172 17936 .104 9.764 3.261 3.287
10 587 204 118 125 469 79 596 189 124 130 478 64 0 0 212 92 36 36 100 61 100 50 548 542 5.937 .168 .134 .208 .21 .124 52 280 .194 .73 80 3630 18570 82 90 254 262 0 352 216 136 .29 326 110 3.443 .231 -1.784 -2.115
11 2388 2106 126 122 2262 1984 2422 2197 131 125 2296 2075 0 0 640 458 41 30 100 100 100 100 4246 4371 1.14 .877 .904 .938 .899 .353 80 441 .827 .96 100 3800 18570 81 91 270 280 0 3631 210 3421 1.512 3788 3578 .661 1.558 .597 .64
12 575 227 121 115 454 112 589 221 125 115 468 106 0 0 151 43 38 24 100 100 100 94 566 574 4.054 .247 .226 .266 .238 .134 52 344 .233 .85 90 3960 18570 81 90 286 295 0 391 198 193 .425 381 183 2.351 .391 -1.233 -1.357
13 427 643 116 116 311 527 146 221 118 120 30 105 0 0 842 1075 33 27 44 98 38 82 838 135 .59 1.695 3.5 4.164 2.668 4.918 52 354 1.257 .95 90 4120 18560 80 89 302 311 0 1109 200 909 2.922 381 181 .342 6.034 1.547 2.593
14 475 133 114 109 361 24 473 134 118 112 359 25 0 0 99 27 32 25 100 50 100 15 385 384 15.042 .066 .07 .099 .083 .068 52 344 .078 .47 90 4280 18570 81 90 318 327 0 229 188 41 .115 231 43 8.724 .12 -3.125 -3.058
15 474 155 114 104 360 51 458 157 119 106 344 53 0 0 92 31 34 24 100 73 100 51 411 397 7.059 .142 .154 .147 .151 .087 52 304 .13 .65 80 4430 18560 81 89 334 342 0 267 179 88 .244 271 91 4.094 .266 -2.034 -1.912
16 547 453 115 106 432 347 543 447 118 106 428 341 0 0 118 69 34 22 100 100 100 100 779 769 1.245 .803 .797 .88 .8 .393 52 370 .736 .9 90 4600 18560 80 89 350 359 0 781 183 598 1.385 771 588 .722 1.374 .47 .458
17 2599 3482 116 103 2483 3379 2595 3669 118 105 2479 3566 0 0 849 975 33 22 100 100 100 100 5862 6045 .735 1.361 1.438 1.411 1.388 .32 52 346 1.272 .97 90 4760 18550 79 88 366 375 0 6003 178 5826 2.346 6326 6148 .426 2.48 1.23 1.31
18 755 652 115 101 640 551 755 660 119 104 640 559 0 0 166 128 39 26 100 100 100 100 1191 1199 1.162 .861 .873 .897 .865 .246 52 359 .751 .94 90 4920 18550 79 88 382 391 0 1124 174 950 1.484 1138 964 .674 1.506 .57 .591
19 1003 886 112 105 891 781 986 904 116 107 874 799 0 0 239 155 37 26 100 100 100 100 1672 1673 1.141 .877 .914 .93 .898 .28 52 344 .81 .94 90 5080 18560 80 89 398 407 0 1528 181 1347 1.511 1559 1378 .662 1.576 .596 .656
20 1242 4694 111 114 1131 4580 1312 4933 118 132 1201 4819 0 0 275 806 52 118 100 100 100 100 5711 6020 .247 4.05 4.012 4.219 3.951 1.016 52 370 3.724 .96 90 5240 18550 79 88 414 423 0 8093 197 7897 6.982 8505 8309 .143 6.918 2.804 2.79

Total number of rows: 21504

Table truncated, full table size 4658 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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