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Sample GSM28860 Query DataSets for GSM28860
Status Public on Jun 13, 2005
Title upf1D_3
Sample type RNA
 
Channel 1
Source name BY4741 (upf1D) @ 26 deg
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
Channel 2
Source name BY4741 (wt) @ 26 deg
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
 
Description Reference and mutant strains grown at 26oC to an OD of 0.5-0.6 . RNA extracted.
 
Submission date Aug 12, 2004
Last update date Jun 13, 2005
Contact name Todd A Burckin
E-mail(s) [email protected]
Phone 831 459-5245
Fax 831 459-3139
Organization name University of California Santa Cruz
Department Molecular, Cell, & Developmental Biology
Lab Hartzog Lab
Street address 1156 High Street
City Santa Cruz
State/province CA
ZIP/Postal code 95062
Country USA
 
Platform ID GPL1370
Series (1)
GSE1684 Exploring functional relationships between components of the gene expression machinery

Data table header descriptions
ID_REF
X X-coordinate of spot
Y Y-coordinate of spot
Dia. spot diameter in microns
F635 Median Channel 2 (Cy5/635) median pixel intensity - feature
F635 Mean Channel 2 (Cy5/635) mean pixel intensity - feature
F635 SD Channel 2 (Cy5/635) standard deviation of pixel intensities - feature
B635 Median Channel 2 (Cy5/635) median background intensity
B635 Mean Channel 2 (Cy5/635) mean background intensity
B635 SD Channel 2 (Cy5/635) standard deviation of background
% > B635+1SD Channel 2 (Cy5/635) percent of pixels 1 StDev above background
% > B635+2SD Channel 2 (Cy5/635) percent of pixels 2 StDevs above background
F635 % Sat. Channel 2 (Cy5/635) percent of pixels saturated
F532 Median Channel 1 (Cy3/532) median pixel intensity - feature
F532 Mean Channel 1 (Cy3/532) mean pixel intensity - feature
F532 SD Channel 1 (Cy3/532) standard deviation of pixel intensities - feature
B532 Median Channel 1 (Cy3/532) median background intensity
B532 Mean Channel 1 (Cy3/532) mean background intensity
B532 SD Channel 1 (Cy3/532) standard deviation of background
% > B532+1SD Channel 1 (Cy3/532) percent of pixels 1 StDev above background
% > B532+2SD Channel 1 (Cy3/532) percent of pixels 2 StDevs above background
F532 % Sat. Channel 1 (Cy3/532) percent of pixels saturated
Ratio of Medians Ratio of medians (Ch2/Ch1)
Ratio of Means Ratio of means (Ch2/Ch1)
Median of Ratios Median of ratios
Mean of Ratios Mean of ratios
Ratios SD Ratio standard deviation
Rgn Ratio Regression ratio
Rgn R? Regression square ratio
F Pixels Number of feature pixels
B Pixels Number of background pixels
Sum of Medians Sum of medians
Sum of Means Sum of means
VALUE Log ratio (base 2)
F635 Median - B635 Channel 2 (Cy5/635) background subtracted median feature intensity
F532 Median - B532 Channel 1 (Cy3/532) background subtracted median feature intensity
F635 Mean - B635 Channel 2 (Cy5/635) background subtracted mean feature intensity
F532 Mean - B532 Channel 1 (Cy3/532) background subtracted mean feature intensity
Flags User defined flag (default=0)

Data table
ID_REF X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1 2170 26300 90 109 156 156 60 61 9 76 69 0 4520 5846 3684 46 48 8 100 100 0 0.011 0.017 0.026 0.028 2.001 0.016 0.34 52 345 4523 5896 -6.513 49 4474 96 5800 0
2 2350 26290 100 69 131 231 61 61 9 47 33 0 62 102 92 46 47 8 63 47 0 0.5 1.25 0.733 0.835 3.539 3.993 0.255 80 487 24 126 -1 8 16 70 56 -100
3 2530 26310 80 100 215 313 61 61 9 98 88 0 117 135 70 46 46 6 100 100 0 0.549 1.73 0.597 0.775 2.355 3.807 0.707 52 292 110 243 -0.864 39 71 154 89 0
4 2700 26290 110 197 278 265 64 64 9 100 100 0 209 216 42 45 46 6 100 100 0 0.811 1.251 0.834 0.954 1.624 2.526 0.509 80 500 297 385 -0.302 133 164 214 171 0
5 2880 26310 100 161 216 188 66 66 9 100 100 0 171 174 36 46 47 7 100 100 0 0.76 1.172 0.819 0.906 1.742 2.653 0.421 80 412 220 278 -0.396 95 125 150 128 0
6 3050 26310 100 15776 15577 2412 66 67 12 100 100 0 17204 16533 3318 47 48 7 100 100 0 0.916 0.941 0.928 0.957 1.163 0.925 0.971 80 400 32867 31997 -0.127 15710 17157 15511 16486 0
7 3230 26280 100 1124 1090 351 65 66 11 100 100 0 1374 1354 337 46 46 7 100 100 0 0.797 0.784 0.772 0.746 1.326 0.804 0.938 80 454 2387 2333 -0.327 1059 1328 1025 1308 0
8 3400 26280 110 1546 1569 202 65 66 11 100 100 0 1753 1730 154 45 45 6 100 100 0 0.867 0.893 0.861 0.89 1.154 0.882 0.943 80 499 3189 3189 -0.206 1481 1708 1504 1685 0
9 3580 26290 110 6193 5645 1831 67 67 11 100 100 0 6695 6381 1993 44 45 6 100 100 0 0.921 0.88 0.889 0.864 1.215 0.886 0.97 80 479 12777 11915 -0.119 6126 6651 5578 6337 0
10 3750 26290 110 1612 1528 374 66 68 13 100 100 0 1930 1851 386 43 44 6 100 100 0 0.819 0.809 0.806 0.794 1.211 0.82 0.96 80 465 3433 3270 -0.288 1546 1887 1462 1808 0
11 3930 26290 110 121 184 188 67 69 13 100 87 0 111 122 54 44 45 6 100 100 0 0.806 1.5 0.824 0.961 2.218 3.276 0.427 80 465 121 195 -0.311 54 67 117 78 0
12 4100 26290 110 211 255 142 68 69 13 100 100 0 258 256 48 44 45 6 100 100 0 0.668 0.882 0.683 0.776 1.545 1.068 0.592 80 431 357 399 -0.582 143 214 187 212 0
13 4280 26290 120 96 121 94 67 68 11 84 64 0 102 104 30 45 45 7 95 92 0 0.509 0.915 0.6 0.619 2.421 2.342 0.419 120 528 86 113 -0.975 29 57 54 59 0
14 4450 26270 100 93 138 141 66 66 10 90 63 0 86 92 25 44 44 7 100 100 0 0.643 1.5 0.689 0.73 2.551 4.347 0.46 80 412 69 120 -0.637 27 42 72 48 0
15 4620 26270 110 1217 1166 247 66 66 10 100 100 0 1226 1145 238 42 43 6 100 100 0 0.972 0.997 0.99 0.996 1.166 0.998 0.963 80 511 2335 2203 -0.041 1151 1184 1100 1103 0
16 4810 26270 100 150 213 233 66 66 10 95 93 0 138 140 51 42 42 6 98 98 0 0.875 1.5 0.934 0.975 2.009 3.479 0.533 80 450 180 245 -0.193 84 96 147 98 0
17 4970 26260 90 109 144 92 67 67 10 98 92 0 97 99 23 42 43 6 100 100 0 0.764 1.351 0.815 0.926 2.014 2.489 0.516 52 356 97 134 -0.389 42 55 77 57 0
18 5150 26250 100 76 94 56 68 70 11 43 27 0 57 58 18 42 43 6 70 52 0 0.533 1.625 1.45 1.134 3.332 3.505 0.393 80 487 23 42 -0.907 8 15 26 16 -50
19 5350 26280 100 266 307 144 68 69 10 100 100 0 241 234 49 42 43 6 100 100 0 0.995 1.245 1.085 1.163 1.36 1.518 0.761 80 394 397 431 -0.007 198 199 239 192 0
20 5490 26260 100 125 168 154 68 69 10 96 93 0 120 128 39 42 43 6 98 98 0 0.731 1.163 0.736 0.801 2.074 2.734 0.476 80 406 135 186 -0.453 57 78 100 86 0

Total number of rows: 5760

Table truncated, full table size 925 Kbytes.




Supplementary data files not provided

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