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Sample GSM11092 Query DataSets for GSM11092
Status Public on Dec 31, 2003
Title VREI_A005_7-22-01
Sample type RNA
 
Channel 1
Source name wt mixed reference mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name TP04 early L4 prep 1 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description TP04 early L4 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
GSE729 TP04 early L4
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 3722 6021 257 131 4053 6276 1922 2694 80 491 2020 15910 110 97 97 100 100 0 0 1 0 1.700 -0.0649173 .562 .956
2678577 544 770 254 114 603 771 333 364 120 479 2180 15910 120 65 40 88 84 0 0 1 0 2.262 0.3470993 .562 1.272
2678579 549 1303 274 121 633 1352 363 722 120 498 2350 15900 120 14 0 89 86 0 0 1 0 4.298 1.2726203 .562 2.416
2678581 1281 26472 243 127 1376 28570 576 7549 80 443 2520 15900 110 67 18 100 100 0 0 1 0 25.381 3.8347113 .562 14.268
2678583 1180 1554 236 124 1280 1664 736 905 120 535 2700 15890 120 87 80 89 87 0 0 1 0 1.515 -0.2310753 .562 .852
2678585 581 3244 253 119 716 3166 483 1533 120 518 2860 15890 120 65 37 93 91 0 0 1 0 9.527 2.4211563 .562 5.356
2678587 1871 9667 231 112 1907 10032 694 2779 80 476 3030 15900 110 100 96 100 100 0 0 1 0 5.826 1.7114953 .562 3.275
2678589 607 729 240 122 622 717 244 251 80 530 3200 15900 110 73 37 100 92 0 0 1 0 1.654 -0.1046973 .562 .930
2678591 568 1127 237 111 614 1162 255 492 32 227 3390 15890 70 84 53 100 96 0 0 1 0 3.069 0.7874323 .562 1.726
2678593 803 1009 268 158 814 1041 431 705 32 148 3530 15870 60 75 59 84 78 0 0 1 0 1.591 -0.1616533 .562 .894
2678595 1582 3059 267 127 1610 2904 631 1067 80 555 3710 15900 110 97 92 98 97 0 0 1 0 2.230 0.3253863 .562 1.253
2678597 714 1055 260 141 714 1020 434 440 32 216 3870 15880 70 59 37 90 84 0 0 1 0 2.013 0.1788743 .562 1.132
2678599 762 1221 288 134 922 1453 582 787 32 214 4060 15870 70 68 50 96 90 0 0 1 0 2.293 0.3662523 .562 1.289
2678601 665 897 254 128 738 928 463 617 80 490 4230 15900 100 62 48 81 75 0 0 1 0 1.871 0.0731353 .562 1.052
2678603 761 1087 240 115 772 1058 427 427 32 209 4410 15870 70 71 59 93 87 0 0 1 0 1.866 0.0690153 .562 1.049
2678605 1502 1972 264 130 1834 2171 1212 1193 80 516 4560 15890 110 97 93 98 98 0 0 1 0 1.488 -0.2584253 .562 .836
2678607 862 3625 276 129 880 3493 390 1432 80 458 4720 15880 100 81 57 93 91 0 0 1 0 5.966 1.7458833 .562 3.354
2678609 586 2189 246 121 585 2097 276 657 80 484 4900 15890 110 61 31 97 97 0 0 1 0 6.082 1.7735743 .562 3.419
2678611 1557 19749 262 123 1568 17090 801 7730 80 419 5060 15880 100 90 86 95 92 0 0 1 0 15.155 3.0908533 .562 8.520
2678613 967 1793 260 116 932 1651 396 680 80 432 5230 15880 100 85 71 91 90 0 0 1 0 2.372 0.4146773 .562 1.333

Total number of rows: 20000

Table truncated, full table size 2192 Kbytes.




Supplementary data files not provided

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