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Sample GSM11056 Query DataSets for GSM11056
Status Public on Dec 31, 2003
Title VREI_SL019_3-20-01
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 2 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description wt L2 prep 2 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 1606 2964 184 221 3090 5638 2964 5520 156 682 2100 17070 140 96 94 95 94 0 0 1 0 1.929 0.9891393 1.029 1.985
2761837 747 1246 184 226 1195 2126 937 1771 208 903 2270 17080 170 97 89 98 97 0 0 1 0 1.812 0.8984023 1.029 1.864
2761839 391 598 191 229 389 586 158 183 52 220 2410 17080 80 78 69 88 86 0 0 1 0 1.845 0.9252403 1.029 1.899
2761841 5261 4291 194 240 4961 4265 1941 1739 52 373 2580 17100 90 100 100 100 100 0 0 1 0 .799 -0.2810363 1.029 .823
2761843 2248 10106 190 238 2125 8904 1411 6239 80 387 2760 17100 100 92 88 100 97 0 0 1 0 4.795 2.3030503 1.029 4.935
2761845 277 325 194 251 446 639 408 732 80 370 2910 17080 110 52 38 33 22 0 0 1 0 .892 -0.1234343 1.029 .918
2761847 2632 3451 191 248 3494 4315 2374 2625 156 824 3060 17080 150 95 94 100 99 0 0 1 0 1.312 0.4329593 1.029 1.350
2761849 848 913 190 235 831 893 305 270 52 299 3250 17090 90 96 94 100 96 0 0 1 0 1.030 0.0840643 1.029 1.060
2761851 18324 911 191 241 24674 1231 18813 835 156 560 3410 17110 140 96 96 83 75 0 0 1 0 .037 -4.7178573 1.029 .038
2761853 1749 2030 191 242 1562 1816 647 707 80 270 3570 17090 100 98 92 98 97 0 0 1 0 1.148 0.2400093 1.029 1.181
2761855 4490 11055 197 252 5484 12709 3788 8138 120 532 3720 17070 130 99 97 100 100 0 0 1 0 2.516 1.3729523 1.029 2.590
2761857 1989 1097 202 261 1790 994 984 474 120 551 3890 17090 130 100 98 96 86 0 0 1 0 .468 -1.0558913 1.029 .481
2761859 283 345 207 259 345 435 331 476 80 445 4040 17090 110 48 27 53 27 0 0 1 0 1.132 0.2203303 1.029 1.165
2761861 529 616 218 267 519 613 133 113 52 344 4210 17100 90 96 82 28 0 0 0 1 0 1.122 0.2078933 1.029 1.155
2761863 582 664 213 270 587 690 215 488 80 425 4370 17100 100 88 82 90 82 0 0 1 0 1.068 0.1361913 1.029 1.099
2761865 1626 1467 219 276 1580 1438 364 250 52 313 4530 17100 90 100 100 100 100 0 0 1 0 .846 -0.1992553 1.029 .871
2761867 5542 13331 226 284 4968 12354 3184 8145 80 433 4690 17090 110 98 98 100 96 0 0 1 0 2.454 1.3368553 1.029 2.526
2761869 666 948 238 291 653 837 246 296 80 318 4850 17100 100 87 80 88 82 0 0 1 0 1.535 0.6599253 1.029 1.580
2761871 1482 1634 238 286 2542 2854 2219 2498 208 827 5000 17110 160 91 87 87 84 0 0 1 0 1.084 0.1570443 1.029 1.115
2761873 5998 1155 241 288 8461 1443 5793 856 156 540 5180 17100 140 97 97 95 88 0 0 1 0 .151 -2.6896603 1.029 .155

Total number of rows: 21632

Table truncated, full table size 2345 Kbytes.




Supplementary data files not provided
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