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Sample GSM11059 Query DataSets for GSM11059
Status Public on Dec 31, 2003
Title VREI_SJ098_3-19-01
Sample type RNA
 
Channel 1
Source name wt mixed reference
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name wt L3 prep 1 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description wt L3 prep 1 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
GSE720 wt L3
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 Ám 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 9675 37283 555 588 8717 31082 4467 16376 52 291 930 17000 80 94 90 100 98 0 0 1 0 4.024 1.5375453 .722 2.903
2761837 4652 8228 567 602 4683 7818 958 2273 52 360 1110 17010 90 100 100 98 96 0 0 1 0 1.867 0.4297503 .722 1.347
2761839 1471 1924 553 594 1439 2010 459 512 52 284 1270 17000 80 90 84 100 98 0 0 1 0 1.449 0.0635033 .722 1.045
2761841 7479 7716 546 588 7478 6982 3456 3146 52 344 1430 17010 90 100 96 98 98 0 0 1 0 1.028 -0.4305093 .722 .742
2761843 4563 38518 586 630 4407 36591 1697 9441 52 364 1590 17000 90 98 94 100 100 0 0 1 0 9.527 2.7811503 .722 6.874
2761845 1410 1799 578 629 1626 2533 874 1853 32 155 1760 16990 60 87 62 68 59 0 0 1 0 1.406 0.0214803 .722 1.015
2761847 4700 11011 588 619 4503 10257 2521 5626 80 456 1910 17000 100 86 85 95 91 0 0 1 0 2.527 0.8671063 .722 1.824
2761849 2080 3114 585 644 2124 3070 535 617 32 220 2080 17000 70 96 96 100 100 0 0 1 0 1.652 0.2533843 .722 1.192
2761851 52490 6171 572 612 50525 5851 9479 1438 52 337 2230 17010 90 100 100 100 100 0 0 1 0 .107 -3.6989983 .722 .077
2761853 2550 3341 568 595 2390 2968 974 1254 80 388 2390 17010 100 91 86 91 87 0 0 1 0 1.385 0.0000003 .722 1.000
2761855 11460 25643 582 598 10084 21626 4740 10405 80 394 2550 17000 100 96 93 100 100 0 0 1 0 2.302 0.7320523 .722 1.661
2761857 3457 2907 545 589 3271 2706 1043 854 80 480 2710 17010 110 96 95 95 90 0 0 1 0 .796 -0.8008773 .722 .574
2761859 9935 11267 554 610 10992 13038 6844 7852 52 315 2880 17000 90 98 96 100 100 0 0 1 0 1.136 -0.2863043 .722 .820
2761861 1249 1603 558 612 1240 1504 471 578 80 416 3030 17010 100 80 68 85 80 0 0 1 0 1.434 0.0496313 .722 1.035
2761863 1397 1847 606 630 1346 1844 520 736 52 296 3200 16990 80 82 61 94 90 0 0 1 0 1.539 0.1505603 .722 1.110
2761865 2440 2775 621 632 2468 2688 775 741 52 323 3360 17010 90 98 96 98 98 0 0 1 0 1.178 -0.2344653 .722 .850
2761867 5340 11315 581 614 6482 14456 4735 11289 80 416 3510 17010 100 92 80 96 87 0 0 1 0 2.249 0.6986633 .722 1.623
2761869 1511 2254 577 602 1570 2147 718 874 80 408 3680 17000 100 87 78 90 86 0 0 1 0 1.769 0.3516283 .722 1.276
2761871 3866 4317 560 589 4219 4788 2944 3338 80 375 3840 17010 100 86 82 92 78 0 0 1 0 1.128 -0.2968993 .722 .814
2761873 12092 3538 566 587 11244 3273 6764 1809 80 384 3990 17010 100 95 93 90 85 0 0 1 0 .256 -2.4344033 .722 .185

Total number of rows: 21632

Table truncated, full table size 2371 Kbytes.




Supplementary data files not provided

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