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Sample GSM12885 Query DataSets for GSM12885
Status Public on Jan 18, 2004
Title Adult 16hr
Sample type RNA
 
Channel 1
Source name CF512 animals, adult age 16hr
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name Reference sample A2
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description We wished to study normal adult aging in C. elegans. We competitively hybridized a series of experimental samples (experimental variable: adult age) against a common reference sample.

We use the CF512 fer-15(b26) II; fem-1 (hc17) IV mutant strain, which has defective spermatids which fail to activate into spermatozoa at 25C. Culturing this strain at 25C prevented self-fertilization and therefore eliminated contributions from embryonic transcripts. CF512 animals develop an otherwise-normal germ line; their lifespan and aging are similar to wild-type animals.

We axenized eggs and then synchronized animals via L1 arrest. Populations were very tightly synchronized. Animals were cultured at 25C. Samples were extracted and hybridized as described in protocols at http://microarrays.org.
Keywords = aging
 
Submission date Nov 11, 2003
Last update date May 28, 2005
Contact name Coleen T Murphy
E-mail(s) cmurphy@worms.ucsf.edu
Phone 415-341-8864
Organization name University of California, San Francisco
Department Biochemistry Department
Lab Kenyon lab
Street address
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL576
Series (1)
GSE832 Adult aging in C. elegans

Data table header descriptions
ID_REF
VALUE Normalized, adjusted log-expression ratio
F635_Median median pixel intensity of feature for Cy5 channel - in this experiment Cy5 channel is normal whole brain (reference) throughout the data set
F635_Mean mean pixel intensity of feature for Cy5 channel
F635_SD Cy5 pixel intensity standard deviation
B635_Median median Cy5 feature background intensity
B635_Mean mean Cy5 feature background intensity
B635_SD Cy5 background pixel intensity standard deviation
Pct_exceeding_B635plus1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
Pct_exceeding_B635plus2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635_Pct_Sat percentage of pixel saturation within feature
F532_Median median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532_Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532_SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532_Median median feature background intensity at wavelength #2 (532 nm, Cy3)
B532_Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532_SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
Pct_exceeding_B532plus1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
Pct_exceeding_B532plus2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
F532_Pct_Sat percentage of feature pixels at wavelength #2 (Cy3) that are saturated
Ratio_of_Medians ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
Ratio_of_Means ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
Median_of_Ratios median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
Mean_of_Ratios arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
Ratios_SD standard deviation of the log of pixel intensity ratios. Note: ratios greater than 100 and less than 0.01 are excluded when calculating this data type
Rgn_Correlationtio regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn_Correlation coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F_Pixels number of feature pixels
B_Pixels number of background pixels
Sum_of_Medians sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Sum_of_Means sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Log_Ratio base two logarithm of the ratio of medians
F635_Median_minus_B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532_Median_minus_B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635_Mean_minus_B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532_Mean_minus_B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags sub-standard features will have a negative value, while a good feature will have a positive value

Data table
ID_REF VALUE F635_Median F635_Mean F635_SD B635_Median B635_Mean B635_SD Pct_exceeding_B635plus1SD Pct_exceeding_B635plus2SD F635_Pct_Sat F532_Median F532_Mean F532_SD B532_Median B532_Mean B532_SD Pct_exceeding_B532plus1SD Pct_exceeding_B532plus2SD F532_Pct_Sat Ratio_of_Medians Ratio_of_Means Median_of_Ratios Mean_of_Ratios Ratios_SD Rgn_Correlationtio Rgn_Correlation F_Pixels B_Pixels Sum_of_Medians Sum_of_Means Log_Ratio F635_Median_minus_B635 F532_Median_minus_B532 F635_Mean_minus_B635 F532_Mean_minus_B532 Flags
1.1.1 -0.093 1737 1713 607 239 332 506 92 76 0 1539 1511 455 291 331 135 100 96 0 1.200 1.208 1.211 1.206 0.266 1.179 0.929 80 534 2746 2694 0.263 1498 1248 1474 1220 0
1.2.1 0.157 7053 6441 2616 219 271 157 100 100 0 5079 4708 1795 290 319 122 100 100 0 1.427 1.408 1.411 1.425 0.323 1.403 0.979 120 568 11623 10640 0.513 6834 4789 6222 4418 0
1.3.1 -0.125 1624 1906 1064 212 225 112 100 100 0 1481 1688 939 278 288 110 100 98 0 1.174 1.201 1.182 1.299 0.434 1.141 0.946 80 479 2615 3104 0.231 1412 1203 1694 1410 0
1.4.1 0.163 7246 7081 2290 260 280 132 100 100 0 5195 4977 1461 321 334 124 100 99 0 1.433 1.465 1.462 1.492 0.334 1.459 0.977 120 512 11860 11477 0.519 6986 4874 6821 4656 0
1.5.1 -0.181 1703 2337 2354 260 276 92 72 63 0 1586 2086 1985 308 318 83 73 63 0 1.129 1.168 1.182 1.411 1.620 1.173 0.978 208 766 2721 3855 0.175 1443 1278 2077 1778 0
1.6.1 468 733 603 268 284 106 52 49 0 486 763 551 314 324 77 57 50 0 1.163 1.036 1.044 2.465 7.410 1.074 0.917 208 786 372 914 0.218 200 172 465 449 -50
1.7.1 0.194 13966 12773 4478 313 321 114 100 100 0 9681 9027 3007 359 363 76 100 100 0 1.465 1.437 1.438 1.440 0.249 1.431 0.982 120 544 22975 21128 0.551 13653 9322 12460 8668 0
1.8.1 -0.128 3134 3245 1310 346 400 207 99 97 0 2772 2753 970 392 445 218 99 98 0 1.171 1.228 1.204 1.215 0.226 1.239 0.973 120 532 5168 5260 0.228 2788 2380 2899 2361 0
1.9.1 0.013 19728 18824 6975 484 545 301 100 100 0 15426 14565 4989 522 583 281 100 100 0 1.291 1.306 1.318 1.320 0.241 1.306 0.980 120 521 34148 32383 0.369 19244 14904 18340 14043 0
1.10.1 0.192 24382 23254 6393 474 504 226 100 100 0 16848 15861 4276 495 530 212 100 100 0 1.462 1.482 1.505 1.547 0.578 1.472 0.983 120 529 40261 38146 0.548 23908 16353 22780 15366 0
1.11.1 0.084 4132 4474 1926 355 377 123 100 99 0 3180 3360 1375 395 417 106 100 99 0 1.356 1.389 1.398 1.416 0.278 1.376 0.974 120 546 6562 7084 0.440 3777 2785 4119 2965 0
1.12.1 -0.143 2777 3263 1757 335 357 112 100 98 0 2487 2710 1271 380 395 91 99 99 0 1.159 1.257 1.216 1.439 1.927 1.269 0.967 120 495 4549 5258 0.213 2442 2107 2928 2330 0
1.13.1 -0.041 9216 9037 3356 412 503 394 100 100 0 7518 7263 2554 441 491 245 100 100 0 1.244 1.264 1.273 1.307 0.391 1.259 0.972 120 543 15881 15447 0.315 8804 7077 8625 6822 0
1.14.1 0.003 7298 8078 5388 395 466 330 96 91 0 5807 6181 4036 427 466 200 98 93 0 1.283 1.335 1.346 1.495 0.791 1.319 0.967 120 540 12283 13437 0.360 6903 5380 7683 5754 0
1.15.1 -0.201 1842 2371 1799 322 349 172 97 91 0 1715 2052 1482 349 368 121 98 91 0 1.113 1.203 1.183 1.463 2.311 1.177 0.946 120 536 2886 3752 0.154 1520 1366 2049 1703 0
1.16.1 -0.165 5235 5046 2566 307 335 173 98 95 0 4637 4265 2057 321 343 114 100 96 0 1.142 1.202 1.238 1.267 0.442 1.192 0.961 120 583 9244 8683 0.191 4928 4316 4739 3944 0
1.17.1 -0.033 4819 4614 1588 299 310 93 99 98 0 3932 3657 1181 318 331 73 100 100 0 1.251 1.292 1.303 1.308 0.340 1.283 0.965 120 534 8134 7654 0.323 4520 3614 4315 3339 0
1.18.1 -0.105 2268 2329 740 281 290 84 100 100 0 1993 2045 607 324 333 73 100 100 0 1.191 1.190 1.163 1.210 0.248 1.177 0.958 120 502 3656 3769 0.252 1987 1669 2048 1721 0
1.19.1 -0.203 1558 1817 1073 278 291 93 99 98 0 1481 1665 817 330 339 89 100 100 0 1.112 1.153 1.119 1.157 0.316 1.184 0.957 120 513 2431 2874 0.153 1280 1151 1539 1335 0
1.20.1 -0.069 6345 6208 2469 270 281 85 100 100 0 5295 5128 1940 318 328 83 100 100 0 1.221 1.235 1.239 1.260 0.307 1.220 0.966 120 521 11052 10748 0.288 6075 4977 5938 4810 0

Total number of rows: 20000

Table truncated, full table size 3283 Kbytes.




Supplementary data files not provided
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