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Sample GSM114132 Query DataSets for GSM114132
Status Public on Aug 01, 2006
Title SWES_C038_03-27-03
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 15 hr unc-79;fem-1 vs reference
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 2070 16620 130 4931 5282 3699 154 196 135 90 90 0 6944 6695 3919 196 223 108 95 91 0 0.708 0.789 0.780 0.731 2.106 0.821 0.819 120 658 11525 11627 -0.498 4777 6748 5128 6499 0
1a2b1c 2250 16610 130 1538 1897 1260 150 188 154 89 87 0 1796 2052 994 192 217 108 98 96 0 0.865 0.939 0.877 0.797 1.810 1.063 0.767 120 503 2992 3607 -0.209 1388 1604 1747 1860 0
1a3b1c 2410 16610 120 1591 1651 1102 149 197 181 86 81 0 1859 1891 1054 196 226 119 90 86 0 0.867 0.886 0.857 0.867 2.580 0.943 0.842 120 412 3105 3197 -0.206 1442 1663 1502 1695 0
1a4b1c 2580 16610 120 2886 3887 3229 157 211 169 90 81 0 4089 4678 3033 205 234 113 95 94 0 0.703 0.834 0.809 0.656 2.484 0.924 0.742 120 443 6613 8203 -0.509 2729 3884 3730 4473 0
1a5b1c 2750 16610 120 727 782 452 194 233 157 84 75 0 969 916 405 239 266 130 85 79 0 0.730 0.869 0.809 0.945 2.467 1.006 0.578 120 462 1263 1265 -0.454 533 730 588 677 0
1a6b1c 2920 16620 130 1117 1140 590 182 229 165 86 83 0 1397 1365 598 236 270 137 90 86 0 0.805 0.849 0.785 0.791 1.879 0.875 0.724 120 471 2096 2087 -0.312 935 1161 958 1129 0
1a7b1c 3090 16620 130 4847 4847 3234 176 216 150 90 86 0 4705 4555 2591 220 252 122 89 89 0 1.041 1.078 1.034 0.976 2.084 1.161 0.774 120 495 9156 9006 0.059 4671 4485 4671 4335 0
1a8b1c 3270 16610 120 1352 1482 956 179 217 148 90 86 0 1592 1656 850 221 250 120 92 90 0 0.856 0.908 0.831 0.824 2.212 0.984 0.792 120 463 2544 2738 -0.225 1173 1371 1303 1435 0
1a9b1c 3430 16600 120 2168 2306 1453 170 218 177 84 80 0 2682 2530 1323 219 250 121 89 87 0 0.811 0.924 0.910 0.801 2.230 0.981 0.823 120 462 4461 4447 -0.302 1998 2463 2136 2311 0
1a10b1c 3600 16610 130 1882 2114 1272 176 229 192 87 83 0 2274 2223 1076 216 253 131 90 90 0 0.829 0.966 0.948 0.922 1.894 1.033 0.852 120 488 3764 3945 -0.271 1706 2058 1938 2007 0
1a11b1c 3770 16610 130 9197 10716 8234 190 243 177 93 90 0 6621 7266 4415 219 262 145 92 90 0 1.407 1.494 1.446 1.401 2.740 1.705 0.835 120 478 15409 17573 0.493 9007 6402 10526 7047 0
1a12b1c 3940 16610 130 4785 4864 3337 190 234 159 93 90 0 4065 4286 2412 224 259 135 91 89 0 1.196 1.151 1.155 1.152 2.027 1.246 0.852 120 461 8436 8736 0.259 4595 3841 4674 4062 0
1a13b1c 4100 16610 130 3446 3077 1769 178 226 167 89 85 0 3232 2910 1554 222 255 135 89 86 0 1.086 1.078 1.083 1.075 2.310 1.099 0.851 120 480 6278 5587 0.119 3268 3010 2899 2688 0
1a14b1c 4280 16600 130 2355 2456 1585 180 226 161 90 83 0 2524 2597 1449 221 251 131 91 87 0 0.944 0.958 0.932 0.873 2.529 1.002 0.852 120 523 4478 4652 -0.082 2175 2303 2276 2376 0
1a15b1c 4450 16600 120 3793 3527 2006 188 232 152 87 85 0 3658 3388 1810 236 267 134 91 88 0 1.053 1.059 1.044 1.028 2.279 1.077 0.870 120 464 7027 6491 0.075 3605 3422 3339 3152 0
1a16b1c 4610 16610 120 3838 3445 2025 203 245 168 85 81 0 3726 3346 1816 238 271 130 90 85 0 1.042 1.043 1.023 1.074 2.035 1.071 0.928 120 448 7123 6350 0.060 3635 3488 3242 3108 0
1a17b1c 4790 16610 130 4728 4433 2293 197 254 198 91 89 0 5930 5326 2707 225 257 127 95 90 0 0.794 0.830 0.806 0.813 2.340 0.829 0.916 120 485 10236 9337 -0.332 4531 5705 4236 5101 0
1a18b1c 4960 16610 130 5081 5166 2916 176 258 417 89 87 0 5777 5972 3340 218 254 180 96 91 0 0.882 0.867 0.821 0.846 2.617 0.866 0.890 120 470 10464 10744 -0.181 4905 5559 4990 5754 0
1a19b1c 5120 16610 130 6078 6473 4290 176 256 414 88 86 0 8048 8280 4567 221 255 179 93 90 0 0.754 0.781 0.771 0.769 2.506 0.811 0.803 120 504 13729 14356 -0.407 5902 7827 6297 8059 0
1a20b1c 5310 16610 120 1802 1808 977 176 236 209 90 82 0 1969 1961 1008 221 248 123 92 87 0 0.930 0.938 0.937 0.942 1.874 0.943 0.888 120 449 3374 3372 -0.104 1626 1748 1632 1740 0

Total number of rows: 19213

Table truncated, full table size 3298 Kbytes.




Supplementary data files not provided
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