NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM11122 Query DataSets for GSM11122
Status Public on Dec 31, 2003
Title VREI_A013_7-24-01
Sample type RNA
 
Channel 1
Source name wt mixed reference mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name TP11 adult w/ emb 2 prep 1 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description TP11 adult w/ emb 2 prep 1 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
GSE736 TP11 adult with emb 2
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
2678575 5079 11980 124 70 5665 13292 3740 6299 80 499 1800 16760 110 98 98 100 100 0 0 1 0 2.404 0.5190393 .596 1.433
2678577 394 392 126 69 477 589 388 480 80 406 1960 16750 100 76 70 92 92 0 0 1 0 1.205 -0.4759363 .596 .719
2678579 595 574 122 70 737 771 527 527 80 469 2140 16760 110 96 88 96 93 0 0 1 0 1.066 -0.6551723 .596 .635
2678581 3536 2884 122 73 3975 2885 2358 1054 80 469 2310 16750 110 97 95 100 100 0 0 1 0 .823 -1.0262053 .596 .491
2678583 1340 4636 126 74 1527 4717 893 1106 80 463 2470 16750 110 100 100 100 100 0 0 1 0 3.758 1.1641433 .596 2.241
2678585 998 1154 125 76 972 1136 598 694 120 550 2650 16750 120 91 85 92 86 0 0 1 0 1.235 -0.4422223 .596 .736
2678587 3254 6438 125 73 3992 8357 2875 5186 80 455 2820 16750 110 100 98 100 100 0 0 1 0 2.034 0.2785803 .596 1.213
2678589 462 795 122 72 610 1127 438 778 80 484 2990 16760 110 91 81 98 96 0 0 1 0 2.126 0.3425553 .596 1.268
2678591 307 491 118 72 347 494 206 287 52 279 3160 16740 80 80 55 92 90 0 0 1 0 2.217 0.4027223 .596 1.322
2678593 446 447 129 68 749 830 677 757 80 432 3330 16760 100 85 76 95 92 0 0 1 0 1.196 -0.4880263 .596 .713
2678595 3262 3146 130 71 4062 3585 2767 1961 80 483 3500 16760 110 98 97 97 97 0 0 1 0 .982 -0.7734913 .596 .585
2678597 836 907 128 72 1021 1039 745 718 80 468 3670 16760 110 96 92 100 100 0 0 1 0 1.179 -0.5084033 .596 .703
2678599 324 398 128 72 399 576 256 438 80 418 3830 16760 100 73 63 93 91 0 0 1 0 1.663 -0.0115883 .596 .992
2678601 486 628 126 70 600 792 410 483 80 474 4010 16760 110 85 76 100 98 0 0 1 0 1.550 -0.1140353 .596 .924
2678603 846 718 118 69 1030 1057 808 826 80 489 4170 16760 110 90 87 95 95 0 0 1 0 .891 -0.9105023 .596 .532
2678605 2563 5219 117 71 3345 5338 1866 2959 80 511 4350 16770 110 100 100 97 95 0 0 1 0 2.105 0.3276873 .596 1.255
2678607 739 980 122 73 974 1299 776 786 80 501 4520 16760 110 91 90 98 97 0 0 1 0 1.470 -0.1909973 .596 .876
2678609 488 700 130 75 650 956 521 637 80 418 4690 16760 100 85 76 95 91 0 0 1 0 1.746 0.0579703 .596 1.041
2678611 4442 7523 137 79 5438 7397 4598 3041 80 483 4860 16770 110 98 98 100 100 0 0 1 0 1.729 0.0440443 .596 1.031
2678613 1332 2686 143 78 1293 2388 607 1011 80 475 5030 16770 110 91 90 100 100 0 0 1 0 2.193 0.3873633 .596 1.308

Total number of rows: 20000

Table truncated, full table size 2221 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap