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Sample GSM114134 Query DataSets for GSM114134
Status Public on Aug 01, 2006
Title SWES_C014_04-27-03
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 1650 16480 140 2431 2682 1940 139 166 120 89 83 0 3719 3602 2456 167 183 82 93 87 0 0.645 0.740 0.714 0.737 1.894 0.746 0.871 156 701 5844 5978 -0.632 2292 3552 2543 3435 0
1a2b1c 1820 16470 130 544 610 347 150 432 3116 0 0 0 908 915 412 193 238 472 69 30 0 0.551 0.637 0.572 0.594 2.034 7.426 0.479 120 451 1109 1182 -0.860 394 715 460 722 0
1a3b1c 2000 16470 130 511 590 320 148 505 3252 0 0 0 891 937 429 193 265 582 58 15 0 0.520 0.594 0.587 0.552 1.709 3.902 0.648 120 437 1061 1186 -0.943 363 698 442 744 0
1a4b1c 2150 16480 130 940 1034 642 147 298 1029 36 5 0 1376 1471 730 192 268 447 90 62 0 0.670 0.694 0.618 0.631 1.888 1.540 0.617 120 413 1977 2166 -0.578 793 1184 887 1279 0
1a5b1c 2330 16470 130 286 300 149 154 217 555 1 0 0 587 551 195 190 218 241 73 23 0 0.332 0.404 0.400 0.414 2.459 0.547 0.311 120 511 529 507 -1.589 132 397 146 361 0
1a6b1c 2500 16470 130 458 505 283 143 163 102 76 69 0 723 710 287 183 194 70 90 87 0 0.583 0.687 0.671 0.611 2.172 0.798 0.616 120 526 855 889 -0.778 315 540 362 527 0
1a7b1c 2670 16470 130 908 1126 824 140 163 105 91 84 0 1374 1541 891 180 193 70 91 90 0 0.643 0.724 0.664 0.663 1.795 0.786 0.793 120 512 1962 2347 -0.637 768 1194 986 1361 0
1a8b1c 2840 16470 130 579 573 295 152 172 109 84 76 0 824 808 330 185 195 73 91 90 0 0.668 0.676 0.608 0.668 2.049 0.727 0.678 120 481 1066 1044 -0.582 427 639 421 623 0
1a9b1c 3020 16470 140 633 706 474 145 166 110 76 68 0 945 947 608 175 183 64 83 78 0 0.634 0.727 0.703 0.707 2.131 0.736 0.774 156 560 1258 1333 -0.658 488 770 561 772 0
1a10b1c 3190 16470 130 633 688 371 146 174 120 88 78 0 945 944 377 178 190 70 97 95 0 0.635 0.708 0.687 0.634 1.839 0.773 0.706 120 444 1254 1308 -0.655 487 767 542 766 0
1a11b1c 3350 16470 130 3373 3716 2485 154 181 127 93 91 0 3164 3303 1946 171 187 72 94 88 0 1.076 1.137 1.106 1.137 1.756 1.196 0.928 120 470 6212 6694 0.105 3219 2993 3562 3132 0
1a12b1c 3530 16470 130 1555 1728 1104 149 176 133 93 91 0 2114 2347 1306 173 193 107 99 96 0 0.724 0.726 0.709 0.692 2.060 0.744 0.798 120 486 3347 3753 -0.465 1406 1941 1579 2174 0
1a13b1c 3700 16480 130 1469 1489 616 141 161 112 98 97 0 1816 1778 657 167 184 80 99 98 0 0.805 0.837 0.818 0.829 1.528 0.850 0.862 120 424 2977 2959 -0.312 1328 1649 1348 1611 0
1a14b1c 3870 16480 140 847 903 609 142 169 117 83 76 0 1254 1197 687 178 191 76 83 78 0 0.655 0.747 0.733 0.773 1.919 0.789 0.828 156 489 1781 1780 -0.610 705 1076 761 1019 0
1a15b1c 4040 16480 140 1499 1548 1104 156 185 133 81 76 0 2020 1938 1242 192 209 95 86 78 0 0.735 0.797 0.774 0.801 1.957 0.830 0.905 156 477 3171 3138 -0.445 1343 1828 1392 1746 0
1a16b1c 4210 16480 140 1317 1494 1149 169 198 147 82 74 0 1476 1656 1144 208 231 108 79 76 0 0.905 0.915 0.908 0.957 2.010 0.957 0.851 156 509 2416 2773 -0.143 1148 1268 1325 1448 0
1a17b1c 4380 16480 130 1855 1883 895 185 220 168 95 94 0 2479 2460 905 212 244 121 99 99 0 0.737 0.755 0.715 0.706 1.414 0.800 0.902 120 449 3937 3946 -0.441 1670 2267 1698 2248 0
1a18b1c 4550 16480 130 2130 2589 1492 191 235 199 97 95 0 2953 3298 1542 214 250 159 99 98 0 0.708 0.778 0.731 0.723 1.504 0.822 0.863 120 478 4678 5482 -0.498 1939 2739 2398 3084 0
1a19b1c 4720 16480 130 2551 2510 1362 174 219 183 95 92 0 3679 3630 1830 202 232 147 98 95 0 0.684 0.681 0.684 0.642 1.536 0.686 0.886 120 486 5854 5764 -0.549 2377 3477 2336 3428 0
1a20b1c 4890 16480 130 1278 1401 715 159 193 140 95 92 0 1617 1673 665 185 204 88 98 97 0 0.781 0.835 0.818 0.772 1.512 0.885 0.853 120 502 2551 2730 -0.356 1119 1432 1242 1488 0

Total number of rows: 19213

Table truncated, full table size 3311 Kbytes.




Supplementary data files not provided
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