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Sample GSM11049 Query DataSets for GSM11049
Status Public on Dec 31, 2003
Title VREI_SJ059_2-19-01
Sample type RNA
 
Channel 1
Source name wt mixed stage reference
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name glp-4 L4 prep 3
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description glp-4 L4 prep 3 vs mixed reference
 
Submission date Oct 09, 2003
Last update date May 28, 2005
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 GPL446
Series (3)
GSE696 Gene expression in germ line
GSE718 glp-4 L4
GSE5069 Expression Profiling of MAP Kinase-Mediated Meiotic Progression in C. elegans

Data table header descriptions
ID_REF
CH1_median Channel 1 (635 nm, Cy5, Reference) median pixel intensity
CH2_median Channel 2 (532 nm, Cy3, Experiment) median pixel intensity
CH1_back Channel 1 Background
CH2_back Channel 2 Background
CH1_MEAN Channel 1 Mean
CH2_MEAN
CH1_SD Channel 1 Standard Deviation
CH2_SD Channel 2 Standard Deviation
pixels Number of pixels used to determine signal.
bpixels Number of pixels used to determine background.
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
diameter diameter in µm of the feature-indicator
%>CH1_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 1
%>CH1_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 1
%>CH2_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 2
%>CH2_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 2
CH1_%Sat percentage of pixel saturation within feature for Channel 1
CH2_%Sat percentage of pixel saturation within feature for Channel 2
QUALITY
flag An extension of GenePix 3.0 flags described at http://twiki.med.yale.edu/twiki/bin/view/YMD/YMDFlagFields
ratio_calc (CH1_median-CH1_back)/(CH2_median-CH2_back)
VALUE log ratio (log2 of PRE_VALUE)
norm_factor Normalization factor calculated as described at http://twiki.med.yale.edu/twiki/bin/view/YMD/NormalizationAndFilterMethods
PRE_VALUE [(Experiment channel median intensity - background)/(Reference channel median intensity - background)]*(norm_factor)

Data table
ID_REF CH1_median CH2_median CH1_back CH2_back CH1_MEAN CH2_MEAN CH1_SD CH2_SD pixels bpixels x y diameter %>CH1_back+1SD %>CH1_back+2SD %>CH2_back+1SD %>CH2_back+2SD CH1_%Sat CH2_%Sat QUALITY flag ratio_calc VALUE norm_factor PRE_VALUE
2761835 7242 25036 921 367 10142 28652 7469 21795 120 573 1150 17840 130 100 96 100 100 0 0 1 0 3.903 2.7576633 1.733 6.763
2761837 5277 5962 908 365 4796 5428 2450 2769 120 413 1310 17830 120 96 92 100 100 0 0 1 0 1.281 1.1505603 1.733 2.220
2761839 1615 846 881 363 1592 779 418 288 80 365 1460 17820 100 90 72 77 73 0 0 1 0 .658 0.1890343 1.733 1.140
2761841 7520 5319 851 350 7731 5405 5170 3565 80 414 1630 17820 100 92 90 98 98 0 0 1 0 .745 0.3684893 1.733 1.291
2761843 4151 21766 841 344 4326 28231 2564 24176 80 479 1790 17820 110 92 90 93 93 0 16 1 0 6.472 3.4873583 1.733 11.215
2761845 1623 578 854 342 1965 1317 1021 1400 32 214 1950 17800 70 84 71 75 59 0 0 1 0 .307 -0.9105023 1.733 .532
2761847 10186 20150 831 337 8980 17799 3303 6836 80 477 2100 17810 110 100 100 100 100 0 0 1 0 2.118 1.8757803 1.733 3.670
2761849 2237 1075 851 353 2128 1009 724 426 80 337 2260 17820 100 88 85 85 78 0 0 1 0 .521 -0.1472023 1.733 .903
2761851 47154 1263 846 356 36555 1197 25041 653 120 548 2410 17800 130 100 100 84 70 11 0 1 0 .020 -4.8783213 1.733 .034
2761853 3508 3433 845 359 3352 3190 1060 1041 80 376 2580 17810 100 97 93 100 100 0 0 1 0 1.154 1.0000003 1.733 2.000
2761855 21792 17198 828 368 17864 14074 9881 8245 120 563 2750 17800 130 100 100 98 98 0 0 1 0 .803 0.4761223 1.733 1.391
2761857 4174 1568 826 370 4028 1534 1305 497 80 353 2900 17810 100 97 95 100 96 0 0 1 0 .358 -0.6896603 1.733 .620
2761859 10937 5041 812 359 11626 6339 8416 5076 80 391 3060 17820 100 91 87 88 86 0 0 1 0 .462 -0.3201263 1.733 .801
2761861 1808 914 802 364 1831 898 451 195 52 324 3220 17810 90 98 94 100 96 0 0 1 0 .547 -0.0785643 1.733 .947
2761863 1824 1293 813 355 1838 1287 592 570 80 428 3380 17800 100 92 80 87 83 0 0 1 0 .928 0.6852673 1.733 1.608
2761865 3203 1427 848 369 3238 1428 533 415 52 334 3540 17800 90 100 100 100 100 0 0 1 0 .449 -0.3621583 1.733 .778
2761867 17754 14816 833 355 14766 13488 8146 7791 80 444 3710 17790 110 100 97 98 96 0 0 1 0 .855 0.5665723 1.733 1.481
2761869 2477 1206 835 345 2410 1163 726 405 80 379 3860 17790 100 96 91 92 90 0 0 1 0 .524 -0.1376483 1.733 .909
2761871 6321 3591 833 358 5770 3308 2628 1677 80 355 4020 17800 100 93 90 92 91 0 0 1 0 .589 0.0299833 1.733 1.021
2761873 13789 2947 796 352 12076 2668 6534 1346 120 579 4170 17790 130 100 100 99 99 0 0 1 0 .200 -1.5311563 1.733 .346

Total number of rows: 21632

Table truncated, full table size 2405 Kbytes.




Supplementary data files not provided
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