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Sample GSM12886 Query DataSets for GSM12886
Status Public on Jan 18, 2004
Title Adult 28hr
Sample type RNA
 
Channel 1
Source name CF512 animals, 28hr adult age
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 -0.796 1118 1236 1077 151 457 1681 34 0 0 1934 1849 1185 528 758 1267 51 18 0 0.688 0.821 0.796 0.794 0.450 0.914 0.876 156 900 2373 2406 -0.540 967 1406 1085 1321 0
1.2.1 -0.096 2929 4190 4386 165 926 2634 53 32 0 3075 3873 3382 600 1151 1938 53 40 0 1.117 1.230 1.189 1.189 0.994 1.290 0.967 80 477 5239 7298 0.159 2764 2475 4025 3273 0
1.3.1 -0.549 895 1267 1162 160 266 803 46 23 0 1511 1772 1089 610 683 561 67 38 0 0.816 0.953 0.891 0.921 0.574 0.988 0.908 80 419 1636 2269 -0.294 735 901 1107 1162 0
1.4.1 0.115 10077 9533 5889 174 713 2269 82 73 0 8242 7749 4363 580 955 1626 86 78 0 1.292 1.305 1.293 1.331 0.572 1.315 0.962 80 537 17565 16528 0.370 9903 7662 9359 7169 0
1.5.1 -0.139 2648 3256 2901 178 788 2258 52 25 0 2819 3332 2512 540 968 1652 62 32 0 1.084 1.102 1.034 1.085 0.447 1.120 0.929 80 537 4749 5870 0.116 2470 2279 3078 2792 0
1.6.1 -0.305 813 936 647 173 411 1065 37 0 0 1161 1255 645 499 667 811 48 12 0 0.967 1.009 1.040 1.366 1.945 0.912 0.859 80 488 1302 1519 -0.049 640 662 763 756 0
1.7.1 0.141 13855 14247 12390 175 908 3989 64 58 0 10832 10417 8560 440 876 2469 66 59 0 1.316 1.410 1.375 1.770 3.563 1.423 0.970 120 574 24072 24049 0.397 13680 10392 14072 9977 0
1.8.1 0.070 2731 3018 2132 186 1087 4012 27 1 0 2463 2820 1829 432 1002 2605 40 5 0 1.253 1.186 1.164 1.434 1.425 1.194 0.925 80 496 4576 5220 0.325 2545 2031 2832 2388 0
1.9.1 0.250 41526 40619 18600 197 2418 8691 91 88 3 29563 27643 12608 459 1892 5697 92 88 0 1.420 1.487 1.488 1.520 0.324 1.468 0.971 80 465 70433 67606 0.506 41329 29104 40422 27184 0
1.10.1 0.339 24634 19797 16629 177 1340 6459 62 56 0 16621 13925 11299 431 1182 4228 62 58 0 1.511 1.454 1.438 1.370 0.594 1.464 0.980 208 864 40647 33114 0.595 24457 16190 19620 13494 0
1.11.1 0.031 3411 3213 2445 174 308 654 70 62 0 3072 2912 2009 418 519 523 70 64 0 1.220 1.219 1.216 1.904 5.806 1.199 0.958 120 537 5891 5533 0.286 3237 2654 3039 2494 0
1.12.1 0.067 3861 4219 2089 179 341 679 100 90 0 3354 3601 1731 410 529 541 98 88 0 1.251 1.266 1.238 1.329 0.340 1.183 0.943 80 467 6626 7231 0.323 3682 2944 4040 3191 0
1.13.1 0.110 10096 10170 7945 200 541 1687 71 69 0 8141 8244 6177 459 707 1273 72 69 0 1.288 1.281 1.271 1.370 0.668 1.254 0.974 120 555 17578 17755 0.365 9896 7682 9970 7785 0
1.14.1 -0.014 8151 7949 5057 219 709 1855 82 73 0 7196 7000 4160 486 889 1532 81 76 0 1.182 1.187 1.205 1.344 0.654 1.153 0.952 80 523 14642 14244 0.241 7932 6710 7730 6514 0
1.15.1 -0.315 1281 1813 1347 193 386 846 66 37 0 1585 1869 1059 452 623 821 68 36 0 0.960 1.143 1.071 1.117 0.480 1.104 0.891 80 490 2221 3037 -0.058 1088 1133 1620 1417 0
1.16.1 -0.025 9704 9149 4751 189 249 287 93 90 0 8557 7764 3677 450 492 250 91 90 0 1.174 1.225 1.239 1.301 0.423 1.227 0.971 120 564 17622 16274 0.231 9515 8107 8960 7314 0
1.17.1 0.183 9488 8707 5011 197 246 379 91 88 0 7318 6763 3550 462 478 138 92 90 0 1.355 1.351 1.378 1.844 3.132 1.347 0.962 120 521 16147 14811 0.438 9291 6856 8510 6301 0
1.18.1 -0.121 2021 1896 1216 194 270 430 77 68 0 2150 2055 1141 486 524 228 78 76 0 1.098 1.085 1.095 1.348 2.052 1.005 0.879 120 538 3491 3271 0.135 1827 1664 1702 1569 0
1.19.1 -0.524 844 843 537 176 225 236 70 58 0 1304 1223 560 499 532 204 73 66 0 0.830 0.921 0.857 1.313 3.794 0.869 0.868 120 551 1473 1391 -0.269 668 805 667 724 0
1.20.1 -0.293 2584 2756 1933 172 200 167 85 82 0 2974 2832 1673 499 519 159 85 85 0 0.975 1.108 1.094 1.216 1.039 1.075 0.932 120 535 4887 4917 -0.037 2412 2475 2584 2333 0

Total number of rows: 20000

Table truncated, full table size 3239 Kbytes.




Supplementary data files not provided
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