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Sample GSM11046 Query DataSets for GSM11046
Status Public on Dec 31, 2003
Title VREI_SJ088_2-19-01
Sample type RNA
 
Channel 1
Source name wt mixed reference
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name glp-4 L3 prep 4
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description glp-4 L3 prep 4 vs wt 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
GSE717 glp-4 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 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 8586 30567 429 251 7777 29853 2679 5183 52 350 1290 17360 90 98 94 100 100 0 0 1 0 3.717 1.9324393 1.027 3.817
2761837 3271 5671 436 221 3133 5734 864 921 52 336 1450 17360 90 98 94 100 100 0 0 1 0 1.922 0.9818533 1.027 1.975
2761839 968 911 398 226 1010 890 247 236 52 333 1610 17370 90 96 96 100 100 0 0 1 0 1.202 0.3033423 1.027 1.234
2761841 4608 4701 400 232 4398 4448 1435 1392 52 363 1770 17370 90 96 96 100 100 0 0 1 0 1.062 0.1256513 1.027 1.091
2761843 3309 20967 404 227 3158 20229 998 4639 52 365 1940 17360 90 100 98 100 100 0 0 1 0 7.139 2.8744043 1.027 7.333
2761845 1477 1362 432 232 1747 2510 1282 2237 32 218 2100 17360 70 78 71 90 90 0 0 1 0 1.081 0.1518593 1.027 1.111
2761847 4430 8320 422 217 3803 7283 1766 3720 80 425 2250 17370 100 92 85 93 91 0 0 1 0 2.022 1.0545013 1.027 2.077
2761849 1829 1449 392 219 1772 1423 502 454 52 333 2420 17370 90 100 100 98 98 0 0 1 0 .856 -0.1860653 1.027 .879
2761851 24839 1576 380 225 21963 1411 8920 601 80 391 2570 17380 100 100 100 91 87 0 0 1 0 .055 -4.1328943 1.027 .057
2761853 2047 1722 372 229 1859 1494 842 688 80 407 2730 17370 100 87 87 90 88 0 0 1 0 .891 -0.1265803 1.027 .916
2761855 11123 22583 372 229 10517 21185 3453 6886 80 469 2900 17370 110 100 100 100 100 0 0 1 0 2.079 1.0949123 1.027 2.136
2761857 2687 1987 382 227 2384 1836 942 676 80 418 3060 17370 100 92 91 100 97 0 0 1 0 .764 -0.3510743 1.027 .784
2761859 8175 6579 391 226 7898 6246 2872 2466 52 334 3220 17380 90 100 100 100 98 0 0 1 0 .816 -0.2549783 1.027 .838
2761861 991 933 393 228 1009 881 262 283 52 323 3380 17390 90 96 94 98 94 0 0 1 0 1.179 0.2761993 1.027 1.211
2761863 1022 1126 422 228 1036 1087 444 534 80 420 3530 17380 100 80 75 82 78 0 0 1 0 1.497 0.6201173 1.027 1.537
2761865 1982 1788 459 233 1999 1751 537 389 52 354 3700 17380 90 98 98 100 100 0 0 1 0 1.021 0.0690153 1.027 1.049
2761867 12123 20180 462 229 11223 18430 2807 6032 52 354 3860 17380 90 100 100 100 100 0 0 1 0 1.711 0.8131143 1.027 1.757
2761869 1621 1676 463 234 1605 1655 382 312 52 344 4020 17380 90 84 25 100 100 0 0 1 0 1.245 0.3550163 1.027 1.279
2761871 4222 4503 464 234 4034 4396 1190 856 52 353 4180 17380 90 100 100 100 100 0 0 1 0 1.136 0.2228053 1.027 1.167
2761873 10089 2248 482 234 9070 2084 3664 814 80 418 4340 17380 100 100 100 100 97 0 0 1 0 .210 -2.2175913 1.027 .215

Total number of rows: 21632

Table truncated, full table size 2381 Kbytes.




Supplementary data files not provided
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