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Sample GSM113895 Query DataSets for GSM113895
Status Public on Aug 01, 2006
Title SWES_C050_04-15-03
Sample type RNA
 
Channel 1
Source name EXP: fem-1 mRNA
Organism Caenorhabditis elegans
Characteristics fem-1 mRNA
Extracted molecule polyA RNA
Label CY3
 
Channel 2
Source name REF: reference mRNA
Organism Caenorhabditis elegans
Characteristics reference mRNA
Extracted molecule polyA RNA
Label CY5
 
 
Description 0 hr unc-79;fem-1 vs reference prep 2
Data processing log base 2 ratio of cy5 to cy3
 
Submission date Jun 12, 2006
Last update date Jun 13, 2006
Contact name Valerie Reinke
E-mail(s) valerie.reinke@yale.edu
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL3861
Series (1)
GSE5069 Expression Profiling of MAP Kinase-Mediated Meiotic Progression in C. elegans

Data table header descriptions
ID_REF
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Dia diameter in µm of the feature-indicator
F635 Median median pixel intensity of feature for Cy5 channel
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
% > B635+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
% > B635+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635 % 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)
% > B532+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
% > B532+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)r
F532 % 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
Rgn Ratio regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn R? 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
VALUE Log ratio
F635 Median - B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532 Median - B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635 Mean - B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532 Mean - B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags A value of -100 means that this spot was bad. A value of -75 means that the ID for this spot is empty. A value of -50 means that this spot cannot be aligned during analysis. A value of 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality tests.

Data table
ID_REF X Y Dia F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1a1b1c 2320 16500 120 5718 6561 4547 93 99 41 98 95 0 3910 4372 2676 204 212 71 93 91 0 1.518 1.552 1.455 1.578 1.715 1.637 0.902 120 605 9331 10636 0.602 5625 3706 6468 4168 0
1a2b1c 2490 16500 120 1169 1276 747 93 97 39 93 91 0 1240 1186 540 202 211 71 93 90 0 1.037 1.202 1.067 1.094 1.879 1.289 0.813 120 528 2114 2167 0.052 1076 1038 1183 984 0
1a3b1c 2670 16490 110 1248 1369 530 93 97 38 100 100 0 1427 1491 359 192 199 62 100 100 0 0.935 0.982 0.980 0.929 1.401 1.084 0.908 80 443 2390 2575 -0.097 1155 1235 1276 1299 0
1a4b1c 2830 16490 110 1938 2436 1364 93 100 40 98 98 0 2769 3120 1306 212 218 70 100 100 0 0.722 0.806 0.828 0.736 1.507 0.978 0.835 80 459 4402 5251 -0.471 1845 2557 2343 2908 0
1a5b1c 3000 16490 120 654 660 413 94 101 52 84 81 0 992 929 454 215 227 82 85 80 0 0.721 0.793 0.758 0.727 2.093 0.831 0.776 120 584 1337 1280 -0.472 560 777 566 714 0
1a6b1c 3180 16490 110 865 900 362 96 103 47 97 96 0 1138 1118 339 215 229 86 98 97 0 0.833 0.890 0.853 0.833 1.527 0.949 0.868 80 490 1692 1707 -0.263 769 923 804 903 0
1a7b1c 3350 16490 110 2296 2726 1243 92 101 63 98 97 0 2245 2407 785 208 219 74 100 100 0 1.082 1.198 1.185 1.108 1.458 1.393 0.885 80 496 4241 4833 0.114 2204 2037 2634 2199 0
1a8b1c 3520 16490 110 1083 1121 440 95 104 100 100 100 0 1273 1324 352 207 217 68 100 100 0 0.927 0.919 0.906 0.880 1.294 0.973 0.901 80 496 2054 2143 -0.110 988 1066 1026 1117 0
1a9b1c 3690 16490 110 1585 1617 606 98 102 38 100 100 0 1837 1761 481 210 219 68 100 100 0 0.914 0.979 0.974 0.931 1.331 1.038 0.941 80 488 3114 3070 -0.130 1487 1627 1519 1551 0
1a10b1c 3860 16490 110 1174 1290 595 94 98 36 100 98 0 1363 1391 435 210 220 73 100 100 0 0.937 1.013 0.968 0.948 1.412 1.116 0.866 80 468 2233 2377 -0.094 1080 1153 1196 1181 0
1a11b1c 4030 16490 120 6976 7287 4776 89 94 35 93 92 0 6485 6296 3532 216 227 82 91 90 0 1.099 1.184 1.161 1.072 1.709 1.329 0.914 120 532 13156 13278 0.136 6887 6269 7198 6080 0
1a12b1c 4200 16500 120 2695 3087 2291 89 105 149 90 88 0 2956 3031 1618 213 225 82 96 91 0 0.950 1.064 0.974 0.899 1.741 1.194 0.916 120 523 5349 5816 -0.074 2606 2743 2998 2818 0
1a13b1c 4370 16510 110 2592 2710 872 95 101 51 100 100 0 2347 2368 583 207 218 99 100 100 0 1.167 1.210 1.178 1.189 1.267 1.274 0.932 80 448 4637 4776 0.223 2497 2140 2615 2161 0
1a14b1c 4540 16510 110 1829 1943 891 95 99 41 100 100 0 1737 1820 567 206 212 63 100 100 0 1.133 1.145 1.092 1.068 1.422 1.225 0.917 80 468 3265 3462 0.180 1734 1531 1848 1614 0
1a15b1c 4710 16510 110 2386 2616 750 92 100 45 100 100 0 2595 2698 658 214 225 74 100 100 0 0.963 1.016 1.010 1.010 1.179 1.045 0.960 80 468 4675 5008 -0.054 2294 2381 2524 2484 0
1a16b1c 4880 16510 110 3025 3232 923 89 98 45 100 100 0 2510 2697 653 214 222 75 100 100 0 1.279 1.266 1.255 1.253 1.187 1.303 0.965 80 468 5232 5626 0.355 2936 2296 3143 2483 0
1a17b1c 5050 16510 110 3066 3152 1028 92 99 40 100 100 0 2900 2991 733 219 228 81 100 100 0 1.109 1.104 1.087 1.081 1.190 1.171 0.958 80 468 5655 5832 0.150 2974 2681 3060 2772 0
1a18b1c 5220 16510 110 4244 4621 2122 93 102 44 100 100 0 4011 4355 1696 223 238 88 100 100 0 1.096 1.096 1.059 1.072 1.138 1.136 0.973 80 482 7939 8660 0.132 4151 3788 4528 4132 0
1a19b1c 5390 16510 110 4945 5199 1971 90 99 42 100 100 0 4542 4716 1562 217 230 75 100 100 0 1.123 1.136 1.110 1.116 1.148 1.188 0.971 80 482 9180 9608 0.167 4855 4325 5109 4499 0
1a20b1c 5560 16510 110 1492 1737 649 94 101 48 100 100 0 1561 1655 486 219 235 93 100 100 0 1.042 1.144 1.163 1.126 1.243 1.188 0.937 80 463 2740 3079 0.059 1398 1342 1643 1436 0

Total number of rows: 19213

Table truncated, full table size 3347 Kbytes.




Supplementary data files not provided
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