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Sample GSM113894 Query DataSets for GSM113894
Status Public on Aug 01, 2006
Title SWES_C037_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 0 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 2090 16450 120 1765 2337 2069 83 94 50 87 81 0 2232 2755 2047 118 130 58 94 90 0 0.796 0.855 0.807 0.620 2.215 0.955 0.884 120 604 3796 4891 -0.330 1682 2114 2254 2637 0
1a2b1c 2260 16460 130 680 720 427 85 102 62 88 85 0 879 847 378 116 135 66 92 90 0 0.780 0.869 0.862 0.775 1.895 0.945 0.800 120 511 1358 1366 -0.359 595 763 635 731 0
1a3b1c 2430 16460 130 563 684 448 91 111 74 88 84 0 744 799 399 132 145 68 92 90 0 0.771 0.889 0.859 0.858 1.791 0.962 0.824 120 494 1084 1260 -0.375 472 612 593 667 0
1a4b1c 2600 16460 130 715 883 666 90 115 141 80 78 0 1606 2054 1386 134 163 211 89 85 0 0.425 0.413 0.433 0.394 2.139 0.421 0.840 120 482 2097 2713 -1.236 625 1472 793 1920 0
1a5b1c 2770 16460 120 332 371 239 90 109 73 81 73 0 524 521 252 128 151 77 81 76 0 0.611 0.715 0.672 0.695 2.014 0.789 0.645 120 467 638 674 -0.710 242 396 281 393 0
1a6b1c 2940 16460 130 495 534 303 97 121 85 85 81 0 698 665 273 133 156 88 90 84 0 0.704 0.821 0.764 0.770 1.952 0.912 0.720 120 523 963 969 -0.505 398 565 437 532 0
1a7b1c 3110 16460 120 1069 1344 1047 93 116 83 90 85 0 1635 1805 1087 136 158 88 95 91 0 0.651 0.750 0.674 0.677 1.991 0.821 0.785 120 449 2475 2920 -0.619 976 1499 1251 1669 0
1a8b1c 3280 16450 120 533 567 345 94 118 85 82 79 0 738 756 355 136 155 77 90 85 0 0.729 0.763 0.781 0.710 1.859 0.822 0.796 120 446 1041 1093 -0.456 439 602 473 620 0
1a9b1c 3440 16450 120 738 765 416 94 118 84 85 83 0 993 992 468 136 151 70 93 90 0 0.751 0.784 0.711 0.692 2.056 0.798 0.835 120 439 1501 1527 -0.412 644 857 671 856 0
1a10b1c 3610 16450 130 775 892 590 93 115 79 90 87 0 938 1017 549 137 154 84 95 85 0 0.851 0.908 0.796 0.832 1.876 0.962 0.790 120 519 1483 1679 -0.232 682 801 799 880 0
1a11b1c 3790 16450 120 2512 2959 2463 96 118 79 89 87 0 4236 4765 3300 141 161 83 97 94 0 0.590 0.619 0.626 0.519 2.144 0.669 0.813 120 478 6511 7487 -0.761 2416 4095 2863 4624 0
1a12b1c 3960 16450 120 1368 1670 1357 98 123 87 88 86 0 1652 1938 1247 139 163 84 94 90 0 0.839 0.874 0.847 0.714 2.153 0.978 0.744 120 472 2783 3371 -0.253 1270 1513 1572 1799 0
1a13b1c 4130 16460 120 1309 1213 726 102 127 92 83 80 0 1410 1278 697 140 171 98 85 81 0 0.950 0.976 0.925 0.886 1.977 1.002 0.849 120 409 2477 2249 -0.073 1207 1270 1111 1138 0
1a14b1c 4290 16450 120 1001 1013 595 95 124 99 86 80 0 1236 1169 602 134 166 104 88 84 0 0.822 0.887 0.911 0.877 2.107 0.916 0.894 120 455 2008 1953 -0.283 906 1102 918 1035 0
1a15b1c 4470 16450 120 1075 1043 617 98 125 95 78 77 0 1243 1124 584 135 165 99 83 83 0 0.882 0.956 0.924 0.891 1.833 0.991 0.841 120 478 2085 1934 -0.182 977 1108 945 989 0
1a16b1c 4640 16460 120 1198 1124 677 99 130 97 85 82 0 1361 1236 678 136 166 97 85 81 0 0.897 0.932 0.919 0.909 1.925 0.954 0.842 120 426 2324 2125 -0.157 1099 1225 1025 1100 0
1a17b1c 4810 16450 120 1075 1239 888 97 126 101 82 80 0 1392 1486 832 129 158 95 89 86 0 0.774 0.842 0.836 0.702 2.214 0.939 0.846 120 422 2241 2499 -0.369 978 1263 1142 1357 0
1a18b1c 4960 16460 130 1541 1696 1041 103 135 113 89 86 0 2067 2228 1177 133 159 87 95 94 0 0.744 0.760 0.751 0.711 1.982 0.783 0.838 120 444 3372 3688 -0.428 1438 1934 1593 2095 0
1a19b1c 5140 16450 130 1875 2037 1278 113 139 97 90 86 0 2230 2602 1546 141 171 98 93 91 0 0.843 0.782 0.810 0.812 2.280 0.788 0.893 120 520 3851 4385 -0.246 1762 2089 1924 2461 0
1a20b1c 5320 16450 120 657 675 391 109 136 94 88 78 0 820 771 366 137 165 97 87 82 0 0.802 0.893 0.850 0.875 1.954 0.951 0.818 120 462 1231 1200 -0.318 548 683 566 634 0

Total number of rows: 19213

Table truncated, full table size 3283 Kbytes.




Supplementary data files not provided

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