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Sample GSM11073 Query DataSets for GSM11073
Status Public on Dec 31, 2003
Title VREI_A042_6-05-02
Sample type RNA
 
Channel 1
Source name wt mixed reference mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name him-5 adult males prep 3 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description him-5 adult males 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 GPL539
Series (3)
GSE696 Gene expression in germ line
GSE723 adult males vs reference
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
2678575 9762 6468 461 344 11304 6894 7006 3920 80 472 2390 15310 100 95 93 97 96 0 0 1 0 .658 -0.8365013 .850 .560
2678577 625 1285 457 347 838 1388 541 848 52 291 2550 15300 80 51 44 92 90 0 0 1 0 5.583 2.2473203 .850 4.748
2678579 1156 3799 463 348 1279 3849 676 1938 80 414 2720 15310 100 86 81 95 91 0 0 1 0 4.980 2.0820213 .850 4.234
2678581 2430 7782 471 346 3237 9699 2415 6655 80 419 2880 15300 100 90 90 93 92 0 0 1 0 3.796 1.6906413 .850 3.228
2678583 3266 3120 469 344 3301 3110 1653 1529 80 427 3060 15310 100 96 91 92 90 0 0 1 0 .992 -0.2446853 .850 .844
2678585 949 13895 457 345 981 13654 452 7607 80 419 3230 15300 100 83 67 98 98 0 0 1 0 27.541 4.5495463 .850 23.418
2678587 5164 5577 471 355 6204 6627 4470 4502 80 427 3390 15310 100 96 93 93 93 0 0 1 0 1.113 -0.0800883 .850 .946
2678589 759 873 476 369 934 1085 549 582 80 446 3570 15310 100 65 52 91 85 0 0 1 0 1.781 0.5983653 .850 1.514
2678591 679 942 483 379 713 1027 293 407 32 170 3720 15310 60 62 46 96 75 0 0 1 0 2.872 1.2880633 .850 2.442
2678593 1189 1115 478 370 1295 1288 784 690 52 328 3900 15310 80 82 69 76 51 0 0 1 0 1.048 -0.1665033 .850 .891
2678595 3213 3523 478 373 3411 3832 1976 2087 80 458 4090 15310 100 91 90 92 91 0 0 1 0 1.152 -0.0306193 .850 .979
2678597 1001 1374 508 376 1121 1513 667 891 52 300 4250 15300 80 63 61 44 11 0 0 1 0 2.024 0.7832473 .850 1.721
2678599 635 935 497 369 710 934 335 372 32 174 4410 15310 60 50 31 84 81 0 0 1 0 4.101 1.8019863 .850 3.487
2678601 1051 1225 492 361 1185 1303 649 672 80 464 4590 15310 100 77 67 93 88 0 0 1 0 1.546 0.3939653 .850 1.314
2678603 732 1213 508 350 927 1337 524 710 80 442 4760 15310 100 66 43 92 88 0 0 1 0 3.853 1.7119353 .850 3.276
2678605 3033 2035 509 339 3511 2566 1869 1435 52 360 4940 15310 90 100 100 100 100 0 0 1 0 .672 -0.8084373 .850 .571
2678607 1499 5129 509 343 1568 5047 803 2410 80 432 5100 15310 100 85 82 93 92 0 0 1 0 4.834 2.0394893 .850 4.111
2678609 799 3483 535 351 1065 4240 678 2889 80 406 5270 15310 100 60 51 92 90 0 0 1 0 11.864 3.3345683 .850 10.088
2678611 4343 30736 534 364 4583 32231 2372 17025 80 418 5430 15310 100 90 86 98 98 0 1 1 0 7.974 2.7612853 .850 6.780
2678613 2230 2602 534 372 2576 2937 1478 1623 80 440 5600 15320 100 95 90 92 91 0 0 1 0 1.315 0.1609203 .850 1.118

Total number of rows: 20000

Table truncated, full table size 2219 Kbytes.




Supplementary data files not provided
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