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Sample GSM11054 Query DataSets for GSM11054
Status Public on Dec 31, 2003
Title VREI_SL021_2-19-01
Sample type RNA
 
Channel 1
Source name wt mixed reference RNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name glp-4 adult prep 4 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description glp-4 adult prep 4 vs 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
GSE715 glp-4 adults
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 4779 11168 503 364 6721 15720 4968 10747 156 769 2060 16940 140 89 85 94 93 0 0 1 0 2.527 1.9927683 1.575 3.980
2761837 2382 2880 521 347 2660 3119 1439 1524 156 595 2230 16970 140 82 53 84 47 0 0 1 0 1.361 1.1003053 1.575 2.144
2761839 1451 1191 514 329 1440 1212 433 349 52 230 2380 16970 80 90 88 98 98 0 0 1 0 .920 0.5350583 1.575 1.449
2761841 2876 1369 532 329 4327 1976 3552 1468 120 590 2540 16950 120 91 85 90 87 0 0 1 0 .444 -0.5166363 1.575 .699
2761843 2089 17313 536 326 3274 26383 2497 22349 120 587 2730 16990 120 86 81 92 90 0 2 1 0 10.938 4.1068513 1.575 17.230
2761845 1179 1261 570 348 1205 1677 273 982 32 137 2880 16970 60 93 71 96 90 0 0 1 0 1.499 1.2400093 1.575 2.362
2761847 3433 7476 540 317 4433 8291 2511 4334 156 865 3030 16960 150 97 96 100 100 0 0 1 0 2.475 1.9627343 1.575 3.898
2761849 1629 1603 613 323 1797 1707 894 894 52 213 3210 16980 80 26 0 98 96 0 0 1 0 1.260 0.9891393 1.575 1.985
2761851 16210 667 596 338 19783 957 15512 615 156 650 3350 16980 140 90 84 69 55 0 0 1 0 .021 -4.9213903 1.575 .033
2761853 2565 1261 580 364 2371 1227 777 380 80 285 3530 16980 100 97 92 93 85 0 0 1 0 .452 -0.4900513 1.575 .712
2761855 8665 10501 571 376 10688 12718 6401 7604 156 685 3680 16960 150 95 94 98 98 0 0 1 0 1.251 0.9789283 1.575 1.971
2761857 2899 1354 566 355 2758 1299 738 352 80 422 3850 16990 110 100 97 97 93 0 0 1 0 .428 -0.5670413 1.575 .675
2761859 1373 460 534 316 1559 558 1001 336 52 332 4000 16990 90 96 92 67 30 0 0 1 0 .172 -1.8889693 1.575 .270
2761861 1137 796 486 314 1116 798 439 316 80 400 4170 16990 100 80 71 87 82 0 0 1 0 .740 0.2215683 1.575 1.166
2761863 1376 1541 468 320 1299 1408 514 621 80 409 4320 16990 100 86 78 86 83 0 0 1 0 1.345 1.0827033 1.575 2.118
2761865 2660 1519 511 342 2566 1552 604 352 52 291 4490 16990 90 98 98 100 100 0 0 1 0 .548 -0.2125683 1.575 .863
2761867 4725 3211 528 335 8468 5070 7121 4151 120 491 4650 16970 120 95 93 91 88 0 0 1 0 .685 0.1096953 1.575 1.079
2761869 2000 1388 545 343 1978 1398 441 234 52 253 4810 16990 90 100 100 100 100 0 0 1 0 .718 0.1775993 1.575 1.131
2761871 2719 1945 525 320 3428 2334 2016 1347 156 725 4960 16980 150 99 96 96 96 0 0 1 0 .741 0.2228053 1.575 1.167
2761873 5841 890 499 320 6664 1009 3713 518 156 662 5130 16980 150 100 100 89 83 0 0 1 0 .107 -2.5734673 1.575 .168

Total number of rows: 21632

Table truncated, full table size 2390 Kbytes.




Supplementary data files not provided
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