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Sample GSM11055 Query DataSets for GSM11055
Status Public on Dec 31, 2003
Title VREI_SJ070_3-19-01
Sample type RNA
 
Channel 1
Source name wt mixed reference mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name wt L2 prep 1 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description wt L2 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
GSE719 wt L2
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 9153 17815 626 444 8094 15416 3544 6748 80 420 1270 17620 110 97 95 100 100 0 0 1 0 2.037 0.9992783 .981 1.999
2761837 3344 3596 608 432 3094 3456 1117 1151 80 406 1430 17610 100 98 97 100 100 0 0 1 0 1.156 0.1826923 .981 1.135
2761839 1195 1082 605 431 1194 1100 307 191 52 352 1610 17610 90 86 61 98 94 0 0 1 0 1.103 0.1150333 .981 1.083
2761841 6612 5127 614 428 6292 4675 1743 1782 52 323 1770 17620 90 100 100 100 100 0 0 1 0 .783 -0.3789443 .981 .769
2761843 5119 34395 600 456 4792 31524 1533 10453 52 357 1920 17610 90 98 98 100 100 0 0 1 0 7.510 2.8818603 .981 7.371
2761845 1087 1015 564 451 1514 1510 971 1400 32 216 2100 17600 70 75 56 59 56 0 0 1 0 1.078 0.0813403 .981 1.058
2761847 5806 6152 557 437 5212 5551 2229 2145 80 433 2240 17600 100 95 93 98 98 0 0 1 0 1.089 0.0962623 .981 1.069
2761849 1799 1431 581 440 1722 1391 550 323 52 256 2410 17600 80 90 90 98 90 0 0 1 0 .814 -0.3255393 .981 .798
2761851 36341 3006 592 461 29548 2420 18209 1309 120 508 2560 17600 120 99 95 0 0 0 0 1 0 .071 -3.8365013 .981 .070
2761853 2047 2127 602 460 2035 1956 639 620 80 375 2730 17600 100 95 92 97 86 0 0 1 0 1.154 0.1788743 .981 1.132
2761855 8832 19008 582 448 7446 16098 3973 8590 120 531 2890 17600 130 98 97 95 93 0 0 1 0 2.250 1.1427403 .981 2.208
2761857 2610 1588 583 450 2492 1464 968 524 80 358 3040 17610 100 93 90 91 82 0 0 1 0 .561 -0.8598763 .981 .551
2761859 8281 7638 572 446 10050 9596 6628 6597 52 333 3210 17610 90 96 94 100 100 0 0 1 0 .933 -0.1265803 .981 .916
2761861 1260 1123 578 464 1270 1109 340 226 52 344 3370 17610 90 96 82 96 90 0 0 1 0 .966 -0.0770413 .981 .948
2761863 1396 1228 561 466 1387 1214 289 209 52 355 3530 17600 90 100 94 100 90 0 0 1 0 .913 -0.1584293 .981 .896
2761865 1847 1695 561 475 1779 1558 798 675 80 416 3700 17590 100 82 78 80 71 0 0 1 0 .949 -0.1031473 .981 .931
2761867 6241 13806 550 473 6253 13211 4032 9091 80 364 3850 17590 100 92 91 98 96 0 0 1 0 2.343 1.2010063 .981 2.299
2761869 1491 1461 556 451 1411 1365 449 448 80 393 4010 17590 100 88 85 88 82 0 0 1 0 1.080 0.0840643 .981 1.060
2761871 4871 4820 532 454 4925 4849 2379 2578 80 368 4170 17600 100 95 92 90 87 0 0 1 0 1.006 -0.0174173 .981 .988
2761873 7825 1892 572 451 7955 1803 4435 814 120 514 4340 17590 120 100 99 85 66 0 0 1 0 .199 -2.3584543 .981 .195

Total number of rows: 21632

Table truncated, full table size 2343 Kbytes.




Supplementary data files not provided
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