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Sample GSM306274 Query DataSets for GSM306274
Status Public on Jul 29, 2008
Title fer-15 (M) 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/2002-07/30517.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 1066 499 130 93 936 406 556 333 137 95 426 240 0 0 1101 506 41 28 94 78 82 73 1342 666 2.305 .434 .563 .621 .431 .988 52 376 .438 .94 90 2250 18980 100 109 104 113 0 960 179 781 .834 640 462 1.199 1.083 -.262 .116
2 1752 537 131 96 1621 441 1761 512 144 109 1630 416 0 0 495 150 78 100 100 100 100 98 2062 2046 3.676 .272 .255 .283 .276 .084 52 355 .242 .81 90 2410 18980 100 109 120 129 0 1033 185 848 .523 985 800 1.911 .491 -.935 -1.027
3 600 132 127 90 473 42 567 129 133 100 440 39 0 0 165 33 46 98 100 1 100 0 515 479 11.262 .089 .089 .107 .096 .06 52 354 .12 .92 90 2570 18980 100 109 136 145 0 254 173 81 .171 248 75 5.856 .17 -2.55 -2.553
4 1280 2040 126 94 1154 1946 1151 2145 146 96 1025 2051 0 0 501 872 166 24 98 100 94 100 3100 3076 .593 1.686 2.001 1.704 1.642 .358 52 299 1.66 .98 80 2730 18980 101 109 153 161 0 3923 181 3742 3.243 4125 3944 .308 3.848 1.697 1.944
5 1203 326 123 96 1080 230 1162 321 133 98 1039 225 0 0 182 57 50 37 100 100 100 100 1310 1264 4.696 .213 .217 .215 .207 .052 52 364 .21 .93 90 2890 18980 100 109 168 177 0 627 185 442 .41 617 433 2.442 .416 -1.288 -1.264
6 1063 868 123 104 940 764 1006 835 127 110 883 731 0 0 605 551 36 47 100 100 96 93 1704 1614 1.23 .813 .828 .81 .788 .323 32 176 .81 .97 60 3050 18980 102 108 186 192 0 1669 200 1469 1.563 1606 1406 .64 1.592 .644 .671
7 3611 1357 124 99 3487 1258 3579 1361 128 102 3455 1262 0 0 458 173 43 27 100 100 100 100 4745 4717 2.772 .361 .365 .363 .364 .046 52 392 .356 .98 90 3210 18970 99 108 200 209 0 2610 190 2419 .694 2617 2427 1.441 .702 -.527 -.51
8 522 165 114 95 408 70 530 163 123 98 416 68 0 0 173 52 52 22 100 75 100 62 478 484 5.829 .172 .163 .184 .172 .127 32 230 .153 .7 70 3380 18980 101 108 218 225 0 317 183 135 .33 313 131 3.031 .314 -1.6 -1.67
9 2176 12171 116 95 2060 12076 2419 14125 125 99 2303 14030 0 0 784 4079 72 27 98 100 97 100 14136 16333 .171 5.862 6.092 6.523 5.903 2.767 80 460 5.629 .98 100 3540 18980 100 110 233 243 0 23406 183 23223 11.273 27163 26981 .089 11.715 3.495 3.55
10 866 272 115 98 751 174 858 271 122 99 743 173 0 0 305 89 53 23 100 100 96 96 925 916 4.316 .232 .233 .271 .232 .17 52 334 .199 .81 90 3700 18980 100 109 249 258 0 523 188 335 .446 521 333 2.244 .448 -1.166 -1.159
11 3535 2481 114 99 3421 2382 4015 2902 127 103 3901 2803 0 0 1484 961 90 38 100 100 100 100 5803 6704 1.436 .696 .719 .733 .692 .251 80 500 .668 .98 110 3860 18970 98 109 264 275 0 4771 190 4581 1.339 5581 5390 .747 1.382 .421 .467
12 732 293 113 102 619 191 749 295 123 105 636 193 0 0 176 64 78 36 100 100 100 96 810 829 3.241 .309 .303 .32 .295 .11 52 296 .288 .91 80 4020 18980 101 109 282 290 0 563 196 367 .593 567 371 1.685 .584 -.753 -.777
13 808 961 113 117 695 844 225 285 137 118 112 168 0 0 1305 1321 223 28 37 78 31 65 1539 280 .823 1.214 1.5 1.909 1.157 1.903 32 157 .867 .86 60 4210 18960 100 106 302 308 0 1848 225 1623 2.335 548 323 .428 2.885 1.224 1.528
14 517 172 115 98 402 74 507 171 127 99 392 73 0 0 95 36 153 25 100 88 86 71 476 465 5.432 .184 .186 .189 .184 .099 52 342 .157 .7 90 4350 18990 101 110 314 323 0 331 188 142 .354 329 140 2.825 .358 -1.498 -1.481
15 527 174 108 84 419 90 531 167 116 86 423 83 0 0 101 47 37 23 100 96 100 82 509 506 4.656 .215 .196 .217 .202 .097 52 364 .188 .75 90 4510 18970 99 108 330 339 0 335 162 173 .413 321 160 2.421 .377 -1.276 -1.406
16 659 442 108 79 551 363 654 462 114 80 546 383 0 0 171 77 33 20 100 100 100 100 914 929 1.518 .659 .701 .695 .66 .174 52 363 .594 .92 90 4670 18970 99 108 346 355 0 850 152 698 1.267 888 737 .789 1.349 .341 .432
17 2777 3675 119 84 2658 3591 2911 3677 125 86 2792 3593 0 0 731 779 48 21 100 100 100 100 6249 6385 .74 1.351 1.287 1.416 1.383 .349 52 363 1.27 .97 90 4830 18980 100 109 362 371 0 7067 162 6906 2.598 7071 6910 .385 2.475 1.377 1.307
18 872 655 117 77 755 578 869 658 117 80 752 581 0 0 154 123 34 20 100 100 100 100 1333 1333 1.306 .766 .773 .784 .778 .181 52 352 .714 .95 90 5000 18970 99 108 379 388 0 1260 148 1112 1.472 1265 1117 .679 1.486 .558 .571
19 982 765 107 73 875 692 960 779 112 76 853 706 0 0 337 229 35 22 97 100 97 100 1567 1559 1.264 .791 .828 1.476 .81 5.096 80 392 .721 .94 100 5150 18980 100 110 394 404 0 1471 140 1331 1.521 1498 1358 .658 1.592 .605 .671
20 1319 4780 110 79 1209 4701 1349 5080 114 86 1239 5001 0 0 348 1177 32 36 100 100 100 100 5910 6240 .257 3.888 4.036 3.999 3.975 .762 52 358 3.597 .97 90 5300 18970 99 108 409 418 0 9192 152 9040 7.478 9769 9617 .134 7.762 2.903 2.956

Total number of rows: 21504

Table truncated, full table size 4687 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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