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Sample GSM114131 Query DataSets for GSM114131
Status Public on Aug 01, 2006
Title SWES_C012_04-27-03
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 1660 16480 140 2013 2513 2090 129 155 107 85 80 0 2094 2417 1770 131 140 54 88 85 0 0.960 1.043 1.020 0.979 2.075 1.112 0.950 156 680 3847 4670 -0.059 1884 1963 2384 2286 0
1a2b1c 1820 16490 140 465 456 218 135 158 105 80 74 0 607 552 244 130 141 55 87 82 0 0.692 0.761 0.770 0.766 2.160 0.803 0.709 156 449 807 743 -0.532 330 477 321 422 0
1a3b1c 2000 16480 140 452 481 261 129 151 89 82 71 0 644 570 265 132 141 53 85 80 0 0.631 0.804 0.780 0.792 2.463 0.874 0.703 156 503 835 790 -0.665 323 512 352 438 0
1a4b1c 2160 16490 130 793 881 437 130 152 93 95 91 0 775 781 270 133 143 52 100 99 0 1.033 1.159 1.155 1.035 1.772 1.292 0.827 120 387 1305 1399 0.046 663 642 751 648 0
1a5b1c 2330 16480 130 382 407 196 135 155 94 82 63 0 548 538 208 132 142 52 95 91 0 0.594 0.670 0.710 0.608 2.489 0.757 0.581 120 485 663 678 -0.752 247 416 272 406 0
1a6b1c 2490 16490 130 464 483 254 138 160 104 78 66 0 683 613 261 134 145 54 88 87 0 0.594 0.720 0.696 0.654 2.007 0.815 0.659 120 485 875 824 -0.752 326 549 345 479 0
1a7b1c 2670 16470 130 924 972 512 136 165 116 90 88 0 1047 1062 484 132 145 59 92 90 0 0.861 0.899 0.879 0.882 1.863 0.995 0.869 120 528 1703 1766 -0.216 788 915 836 930 0
1a8b1c 2840 16480 130 559 598 226 142 166 106 96 85 0 722 705 194 132 146 60 96 95 0 0.707 0.796 0.828 0.755 1.650 0.879 0.715 120 489 1007 1029 -0.501 417 590 456 573 0
1a9b1c 3020 16480 140 678 685 412 147 167 106 80 71 0 936 829 448 131 146 63 83 79 0 0.660 0.771 0.793 0.774 2.118 0.837 0.819 156 536 1336 1236 -0.600 531 805 538 698 0
1a10b1c 3180 16480 140 496 525 304 144 168 109 75 64 0 650 590 306 131 145 59 83 78 0 0.678 0.830 0.791 0.834 1.925 0.905 0.748 156 483 871 840 -0.560 352 519 381 459 0
1a11b1c 3350 16480 140 2467 2938 2543 143 157 86 85 81 0 1340 1393 947 129 140 51 87 82 0 1.919 2.211 1.982 1.841 1.749 2.502 0.940 156 483 3535 4059 0.940 2324 1211 2795 1264 0
1a12b1c 3520 16480 140 1118 1386 1070 142 160 94 82 80 0 1005 1056 650 131 142 53 86 82 0 1.117 1.345 1.271 1.246 1.782 1.506 0.911 156 521 1850 2169 0.159 976 874 1244 925 0
1a13b1c 3700 16480 130 652 680 326 144 161 98 90 81 0 708 669 254 134 144 55 95 91 0 0.885 1.002 1.014 0.984 1.956 1.139 0.763 120 446 1082 1071 -0.176 508 574 536 535 0
1a14b1c 3860 16490 140 579 588 339 151 162 94 81 70 0 652 601 293 135 144 56 85 78 0 0.828 0.938 0.979 0.966 2.165 1.040 0.791 156 511 945 903 -0.273 428 517 437 466 0
1a15b1c 4030 16480 130 1583 1540 750 153 167 89 92 88 0 1329 1260 507 131 146 59 94 91 0 1.194 1.229 1.251 1.164 1.782 1.344 0.901 120 441 2628 2516 0.255 1430 1198 1387 1129 0
1a16b1c 4200 16490 140 913 949 592 151 173 112 80 74 0 893 806 431 136 152 67 83 77 0 1.007 1.191 1.177 1.153 1.824 1.290 0.865 156 483 1519 1468 0.009 762 757 798 670 0
1a17b1c 4370 16490 140 1014 1046 610 151 182 148 82 78 0 1000 994 528 142 159 75 88 82 0 1.006 1.050 1.059 1.066 1.884 1.108 0.888 156 492 1721 1747 0.008 863 858 895 852 0
1a18b1c 4540 16490 140 1252 1377 1055 155 175 133 81 78 0 1680 1664 1090 143 160 77 85 83 0 0.714 0.803 0.777 0.818 1.804 0.879 0.887 156 510 2634 2743 -0.487 1097 1537 1222 1521 0
1a19b1c 4710 16480 130 1784 2075 1309 146 165 93 91 91 0 2113 2338 1293 142 154 68 93 92 0 0.831 0.878 0.908 0.876 1.600 0.952 0.940 120 460 3609 4125 -0.267 1638 1971 1929 2196 0
1a20b1c 4880 16490 140 678 655 366 144 167 105 81 76 0 736 684 313 140 154 69 86 81 0 0.896 0.939 0.966 0.917 2.094 1.035 0.794 156 527 1130 1055 -0.158 534 596 511 544 0

Total number of rows: 19213

Table truncated, full table size 3225 Kbytes.




Supplementary data files not provided

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