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Sample GSM114130 Query DataSets for GSM114130
Status Public on Aug 01, 2006
Title SWES_C020_04-14-03
Sample type RNA
 
Channel 1
Source name EXP: mpk-1 mRNA
Organism Caenorhabditis elegans
Characteristics mpk-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-79mpk-1;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 1590 16490 130 3613 4250 3136 131 148 94 90 88 0 6825 7072 4326 140 151 59 92 92 0 0.521 0.594 0.559 0.521 1.728 0.679 0.884 120 600 10167 11051 -0.941 3482 6685 4119 6932 0
1a2b1c 1760 16500 140 1110 1260 995 138 164 119 82 75 0 1423 1428 944 147 163 72 84 80 0 0.762 0.876 0.806 0.869 2.432 0.956 0.854 156 495 2248 2403 -0.393 972 1276 1122 1281 0
1a3b1c 1930 16500 130 1228 1579 1052 144 184 276 89 83 0 1505 1651 878 154 208 477 88 70 0 0.802 0.959 0.834 0.908 1.715 1.048 0.784 120 431 2435 2932 -0.318 1084 1351 1435 1497 0
1a4b1c 2100 16490 130 1921 2372 1816 154 186 256 85 84 0 2372 2760 1770 157 203 442 88 82 0 0.798 0.852 0.785 0.760 1.744 0.978 0.882 120 503 3982 4821 -0.326 1767 2215 2218 2603 0
1a5b1c 2270 16490 120 445 499 325 153 176 123 77 60 0 701 630 269 151 168 75 90 80 0 0.531 0.722 0.660 0.687 2.056 1.012 0.602 120 457 842 825 -0.913 292 550 346 479 0
1a6b1c 2440 16500 130 762 935 544 138 161 108 90 86 0 1062 1064 495 154 167 70 92 91 0 0.687 0.876 0.765 0.811 1.841 0.947 0.776 120 496 1532 1707 -0.541 624 908 797 910 0
1a7b1c 2610 16490 130 2569 3392 2519 150 178 139 90 87 0 2498 2757 1641 154 174 81 92 89 0 1.032 1.245 1.142 1.156 1.839 1.429 0.856 120 536 4763 5845 0.045 2419 2344 3242 2603 0
1a8b1c 2780 16490 130 1014 1107 614 153 191 160 90 82 0 1241 1369 733 162 184 91 90 87 0 0.798 0.790 0.753 0.809 1.752 0.805 0.834 120 536 1940 2161 -0.326 861 1079 954 1207 0
1a9b1c 2950 16500 130 1886 2066 1104 149 184 141 90 90 0 2672 2677 1309 153 171 76 95 91 0 0.690 0.760 0.707 0.749 1.609 0.771 0.867 120 497 4256 4441 -0.536 1737 2519 1917 2524 0
1a10b1c 3120 16500 130 1548 1636 972 138 170 118 92 91 0 1880 1899 1072 156 172 73 93 90 0 0.818 0.859 0.798 0.890 1.806 0.860 0.869 120 489 3134 3241 -0.290 1410 1724 1498 1743 0
1a11b1c 3300 16490 130 7691 8859 6324 137 162 97 95 93 0 7790 8453 4896 150 168 74 98 93 0 0.989 1.050 0.957 0.933 1.822 1.162 0.853 120 489 15194 17025 -0.016 7554 7640 8722 8303 0
1a12b1c 3460 16500 130 2616 3584 2416 149 177 124 96 93 0 3438 4127 2429 151 172 79 95 93 0 0.751 0.864 0.809 0.930 2.153 0.904 0.855 120 461 5754 7411 -0.414 2467 3287 3435 3976 0
1a13b1c 3630 16510 130 2193 2241 1342 150 179 126 90 87 0 2619 2447 1320 154 174 82 88 88 0 0.829 0.912 0.864 0.962 1.656 0.942 0.855 120 480 4508 4384 -0.271 2043 2465 2091 2293 0
1a14b1c 3800 16510 130 1892 2000 1183 144 174 116 87 86 0 2208 2215 1284 148 174 86 87 87 0 0.849 0.898 0.875 0.858 1.708 0.903 0.918 120 488 3808 3923 -0.237 1748 2060 1856 2067 0
1a15b1c 3980 16500 130 2551 2595 1253 148 179 126 95 91 0 4210 4008 1766 156 178 85 99 97 0 0.593 0.635 0.623 0.590 1.519 0.642 0.927 120 512 6457 6299 -0.755 2403 4054 2447 3852 0
1a16b1c 4150 16500 130 2392 2586 1479 148 178 117 93 91 0 3098 3053 1546 161 178 85 95 95 0 0.764 0.843 0.810 0.791 1.860 0.872 0.903 120 491 5181 5330 -0.388 2244 2937 2438 2892 0
1a17b1c 4310 16510 130 3153 3237 1647 148 182 138 95 90 0 4111 4109 2006 157 180 96 94 90 0 0.760 0.782 0.740 0.836 1.788 0.781 0.919 120 455 6959 7041 -0.396 3005 3954 3089 3952 0
1a18b1c 4480 16500 130 3267 3438 2130 142 166 126 93 90 0 4208 4341 2358 149 170 83 98 95 0 0.770 0.786 0.748 0.725 1.668 0.814 0.889 120 514 7184 7488 -0.377 3125 4059 3296 4192 0
1a19b1c 4660 16500 130 4710 5238 3146 138 165 108 95 95 0 7270 7663 3965 154 171 77 99 99 0 0.642 0.679 0.637 0.629 1.722 0.701 0.911 120 494 11688 12609 -0.638 4572 7116 5100 7509 0
1a20b1c 4820 16500 130 1478 1568 815 141 173 112 94 92 0 1874 1807 844 158 174 79 97 94 0 0.779 0.865 0.796 0.868 1.637 0.880 0.843 120 494 3053 3076 -0.360 1337 1716 1427 1649 0

Total number of rows: 19213

Table truncated, full table size 3324 Kbytes.




Supplementary data files not provided
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