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Sample GSM306269 Query DataSets for GSM306269
Status Public on Jul 29, 2008
Title age-1; 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 age-1; fer-15
Organism Caenorhabditis elegans
Characteristics age-1; 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/2002-07/30513.gif
Place of growth: Stanford
Genotype: age-1; 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 (2)
GSE12094 Aging study
GSE12166 TJ411(fer-15(b26)II; age-1(hx542)II) 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 1852 743 175 156 1677 587 1097 486 180 160 922 330 0 0 1870 589 54 38 98 90 93 85 2264 1252 2.857 .35 .358 .577 .375 .705 80 448 .308 .94 100 2550 18320 83 93 142 152 0 1429 300 1129 .673 935 635 1.486 .688 -.571 -.539
2 2142 559 182 160 1960 399 2251 553 188 165 2069 393 0 0 590 141 56 37 100 100 100 100 2359 2462 4.912 .204 .19 .211 .196 .073 52 330 .181 .91 90 2700 18320 83 92 157 166 0 1075 308 767 .391 1063 756 2.554 .365 -1.353 -1.453
3 761 192 176 161 585 31 706 195 184 163 530 34 0 0 212 50 54 41 100 44 100 15 616 564 18.871 .053 .064 .113 .109 .064 52 362 .054 .32 90 2870 18320 83 92 174 183 0 369 310 60 .102 375 65 9.813 .123 -3.295 -3.019
4 1710 2420 169 159 1541 2261 1634 2444 177 163 1465 2285 0 0 576 707 50 39 100 100 100 100 3802 3750 .682 1.467 1.56 1.637 1.513 .798 52 298 1.349 .96 80 3030 18320 84 92 191 199 0 4654 306 4348 2.822 4700 4394 .354 2.999 1.497 1.585
5 1712 477 167 142 1545 335 1696 451 175 146 1529 309 0 0 448 143 51 37 100 100 100 100 1880 1838 4.612 .217 .202 .223 .206 .073 52 372 .201 .9 90 3190 18320 83 92 206 215 0 917 273 644 .417 867 594 2.398 .389 -1.262 -1.363
6 1513 1209 168 125 1345 1084 1802 1402 172 130 1634 1277 0 0 798 717 48 37 100 100 96 100 2429 2911 1.241 .806 .782 1.058 .786 1.641 32 231 .797 .95 70 3360 18320 84 91 224 231 0 2325 240 2085 1.55 2696 2456 .645 1.503 .632 .588
7 3434 1230 162 147 3272 1083 3546 1267 183 151 3384 1120 0 0 608 191 110 41 100 100 100 100 4355 4504 3.021 .331 .331 .338 .332 .063 52 377 .308 .97 90 3510 18310 82 91 238 247 0 2365 283 2083 .637 2437 2154 1.571 .636 -.652 -.652
8 800 346 162 165 638 181 807 322 170 169 645 157 0 0 303 145 46 43 100 81 100 75 819 802 3.525 .284 .243 .332 .335 .216 32 230 .234 .66 70 3680 18320 84 91 256 263 0 665 317 348 .546 619 302 1.833 .468 -.874 -1.095
9 3192 17768 167 165 3025 17603 3411 17997 183 206 3244 17832 0 0 889 3554 87 250 100 100 100 100 20628 21076 .172 5.819 5.497 6.298 5.703 2 52 363 5.37 .97 90 3830 18320 83 92 270 279 0 34169 317 33852 11.191 34610 34292 .089 10.571 3.484 3.402
10 1010 418 169 161 841 257 1032 411 182 186 863 250 0 0 587 192 79 180 86 63 82 30 1098 1113 3.272 .306 .29 .416 .304 .516 52 298 .276 .87 80 4000 18330 85 93 288 296 0 804 310 494 .588 790 481 1.702 .557 -.767 -.844
11 4042 2357 163 161 3879 2196 4132 2486 171 164 3969 2325 0 0 1587 928 53 40 100 100 100 100 6075 6294 1.766 .566 .586 .59 .572 .222 80 441 .543 .96 100 4170 18330 84 94 304 314 0 4533 310 4223 1.089 4781 4471 .919 1.127 .123 .172
12 1009 372 167 165 842 207 995 357 176 166 828 192 0 0 290 144 60 40 100 90 100 82 1049 1020 4.068 .246 .232 .255 .248 .108 52 335 .255 .82 90 4330 18320 83 92 320 329 0 715 317 398 .473 687 369 2.115 .446 -1.081 -1.165
13 784 873 163 165 621 708 241 311 171 165 78 146 0 0 1768 1766 54 39 68 93 37 82 1329 224 .877 1.14 1.872 4.187 1.66 9.975 80 421 .925 .92 100 4490 18320 83 93 336 346 0 1679 317 1362 2.192 598 281 .456 3.6 1.133 1.848
14 817 281 163 167 654 114 827 259 172 171 664 92 0 0 136 78 51 40 100 80 100 61 768 756 5.737 .174 .139 .182 .171 .108 52 335 .163 .68 90 4650 18340 85 94 352 361 0 540 321 219 .335 498 177 2.983 .266 -1.577 -1.908
15 821 278 160 164 661 114 795 273 166 169 635 109 0 0 223 78 47 40 100 80 100 67 775 744 5.798 .172 .172 .21 .191 .14 52 352 .14 .6 90 4800 18330 84 93 367 376 0 535 315 219 .332 525 210 3.015 .33 -1.592 -1.599
16 953 551 169 169 784 382 950 529 176 172 781 360 0 0 178 97 55 42 100 100 100 100 1166 1141 2.052 .487 .461 .51 .468 .171 52 352 .444 .88 90 4970 18330 84 93 384 393 0 1060 325 735 .937 1017 692 1.067 .886 -.094 -.174
17 4714 4727 168 170 4546 4557 5181 4741 174 176 5013 4571 0 0 1961 1737 47 45 100 100 98 100 9103 9584 .998 1.002 .912 1.559 .995 2.06 80 440 .949 .97 100 5130 18330 84 94 400 410 0 9090 327 8763 1.928 9117 8790 .519 1.754 .947 .81
18 1440 1181 166 172 1274 1009 1439 1174 175 180 1273 1002 0 0 263 257 54 55 100 100 100 100 2283 2275 1.263 .792 .787 .801 .815 .19 52 349 .766 .95 90 5300 18330 84 93 417 426 0 2271 331 1940 1.523 2258 1927 .657 1.514 .607 .598
19 1607 952 165 166 1442 786 1597 934 171 170 1432 768 0 0 346 184 47 42 100 100 100 100 2228 2200 1.835 .545 .536 .569 .542 .172 52 334 .504 .92 90 5460 18340 85 94 433 442 0 1831 319 1512 1.048 1796 1477 .954 1.031 .068 .045
20 1851 6118 167 167 1684 5951 2008 6562 177 169 1841 6395 0 0 738 2003 52 41 95 100 92 100 7635 8236 .283 3.534 3.474 4.738 3.522 4.951 80 430 3.273 .97 100 5610 18330 84 94 448 458 0 11765 321 11444 6.796 12619 12298 .147 6.68 2.765 2.74

Total number of rows: 21504

Table truncated, full table size 4811 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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