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Sample GSM11087 Query DataSets for GSM11087
Status Public on Dec 31, 2003
Title VREI_A028_7-29-01
Sample type RNA
 
Channel 1
Source name wt mixed reference mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name TP02 late L3 prep 3 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description TP02 late L3 prep 3 hermaphrodites vs mixed reference
 
Submission date Oct 10, 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
GSE727 TP02 late-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 Ám 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 5310 5755 175 131 7076 7650 4851 4941 80 459 1450 16030 100 98 98 100 100 0 0 1 0 1.095 0.0607393 .953 1.043
2678577 1795 1756 174 131 1878 1964 1394 1461 52 322 1610 16040 90 96 92 100 98 0 0 1 0 1.002 -0.0664273 .953 .955
2678579 1436 1463 169 124 1791 2075 1316 1615 80 439 1780 16030 100 90 88 95 92 0 0 1 0 1.057 0.0100643 .953 1.007
2678581 2141 2147 164 126 3292 3713 2731 2924 80 474 1960 16030 110 98 95 100 100 0 0 1 0 1.022 -0.0380063 .953 .974
2678583 2756 3373 167 126 3409 4001 1947 2331 80 474 2130 16030 110 100 100 98 98 0 0 1 0 1.254 0.2570113 .953 1.195
2678585 2130 1423 175 131 2367 1578 1672 1242 80 461 2300 16030 110 98 97 97 97 0 0 1 0 .661 -0.6665763 .953 .630
2678587 3035 6886 176 130 5428 10472 4513 8035 80 444 2460 16030 100 92 91 98 96 0 0 1 0 2.363 1.1705663 .953 2.251
2678589 1757 1468 161 129 1621 1701 1080 1285 52 288 2660 16040 80 92 88 88 84 0 0 1 0 .839 -0.3237333 .953 .799
2678591 1024 979 176 128 982 1083 635 741 52 278 2800 16020 80 82 76 94 88 0 0 1 0 1.004 -0.0649173 .953 .956
2678593 504 551 188 137 1194 1168 1208 1207 80 430 2970 16050 100 86 76 87 83 0 0 1 0 1.310 0.3196183 .953 1.248
2678595 2951 3491 186 130 3832 4462 2757 3112 80 454 3140 16040 100 95 93 98 97 0 0 1 0 1.216 0.2116353 .953 1.158
2678597 737 794 190 131 1350 1334 1143 1156 80 500 3320 16040 110 98 96 95 92 0 0 1 0 1.212 0.2078933 .953 1.155
2678599 828 971 194 128 1052 1185 790 968 52 295 3470 16040 80 90 78 88 76 0 0 1 0 1.330 0.3414173 .953 1.267
2678601 1334 1142 184 126 1647 1663 1124 1201 80 532 3660 16050 110 95 95 92 91 0 0 1 0 .883 -0.2481083 .953 .842
2678603 1681 1818 184 132 1568 1715 953 1174 52 354 3830 16050 90 98 98 98 80 0 0 1 0 1.126 0.1016503 .953 1.073
2678605 2182 2221 194 128 3672 3465 3116 2843 80 444 4000 16050 100 92 92 98 93 0 0 1 0 1.053 0.0043223 .953 1.003
2678607 1256 1504 185 130 1905 2094 1492 1583 80 432 4170 16050 100 93 90 93 90 0 0 1 0 1.283 0.2892443 .953 1.222
2678609 1418 1418 172 124 1476 1451 1074 1040 52 353 4330 16050 90 96 92 100 100 0 0 1 0 1.039 -0.0159583 .953 .989
2678611 6018 22187 192 131 5259 18718 2424 8691 80 427 4500 16060 100 97 97 97 97 0 0 1 0 3.786 1.8503993 .953 3.606
2678613 2203 2529 199 132 2170 2540 1109 1305 80 428 4670 16060 100 97 96 95 92 0 0 1 0 1.196 0.1877683 .953 1.139

Total number of rows: 20000

Table truncated, full table size 2243 Kbytes.




Supplementary data files not provided

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