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Sample GSM95382 Query DataSets for GSM95382
Status Public on Mar 17, 2006
Title MC2A_G2_Rerep_UbP11_172_RME5-27_G2_Galp_vs_MCrerepN2_0
Sample type genomic
 
Channel 1
Source name G2 phase re-replicating DNA MC2A
Organism Saccharomyces cerevisiae
Characteristics YJL4489 180 minutes after galactose induction while arrested at G2 phase
Extracted molecule genomic DNA
Label Cy5
Label protocol amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
 
Channel 2
Source name G2 phase non-re-replicating DNA M
Organism Saccharomyces cerevisiae
Characteristics YJL4486 180 minutes after galactose induction while arrested at G2 phase
Extracted molecule genomic DNA
Label Cy3
Label protocol amino-allyl-dUTP incorporation with Klenow. Chemical coupling of dye to aa-dUTP labelled DNA.
 
 
Hybridization protocol Hybridization was performed in 3X SSC, 25mM HEPES pH7.0, 0.25% SDS at 63oC for 24 hours.
Scan protocol Arrays were scanned with an Axon 3000B scanner using GenePix4.0.
Description Data from Figure 6E of MBoC paper (citation coming soon)
Data processing Data were filtered in GenePix to flag as bad features that had (1) obvious defects, (2) saturated pixels, (3) regression r^2 values less than 0.5 or (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to the DNA content of the replicating cells as determined by flow cytometry. The DNA content was 2.0C.
 
Submission date Feb 02, 2006
Last update date Mar 17, 2006
Contact name Joachim J Li
E-mail(s) [email protected]
Phone 415-476-8782
Fax 415-514-4080
Organization name University of California, San Francisco
Department Microbiology and Immunology
Lab Li
Street address 600 16th Street S376
City San Francisco
State/province CA
ZIP/Postal code 94143-2200
Country USA
 
Platform ID GPL3412
Series (1)
GSE4181 Genome-wide mapping of DNA re-replication in S. cerevisiae

Data table header descriptions
ID_REF
PRE_VALUE Cy5/Cy3 ratio normalized to DNA content determined by flow cytometry (NOT a log value)
VALUE log2 of PRE_VALUE
Median of Ratios (635/532) GenePix raw Cy5/Cy3 ratio
Rgn R^2 (635/532) GenePix coefficient of determination for the current regression value for wavelengths 1 and 2
GenePix Flags GenePix flag used to mark the quality of a feature (0 = Good, <0 = Bad)
Dia. GenePix diameter in �m of the feature-indicator
F635 Median GenePix median feature pixel intensity at wavelength 635
F635 Mean GenePix mean feature pixel intensity at wavelength 635
F635 SD GenePix standard deviation of the feature pixel intensity at wavelength 635
B635 Median GenePix median background intensity at wavelength 635
B635 Mean GenePix mean background intensity at wavelength 635
B635 SD GenePix standard deviation of the local background intensity at wavelength 635
% > B635+1SD GenePix percentage of feature pixels with intensities more than one standard deviation above the background intensity, at wavelength 635
% > B635+2SD GenePix percentage of feature pixels with intensities more than two standard deviations above the background intensity, at wavelength 635
F635 % Sat. GenePix percentage of feature pixels at wavelength 635 that are saturated
F532 Median GenePix median feature pixel intensity at wavelength 532
F532 Mean GenePix mean feature pixel intensity at wavelength 532
F532 SD GenePix standard deviation of the feature pixel intensity at wavelength 532
B532 Median GenePix median background intensity at wavelength 532
B532 Mean GenePix mean background intensity at wavelength 532
B532 SD GenePix standard deviation of the local background intensity at wavelength 532
% > B532+1SD GenePix percentage of feature pixels with intensities more than one standard deviation above the background intensity, at wavelength 532
% > B532+2SD GenePix percentage of feature pixels with intensities more than two standard deviations above the background intensity, at wavelength 532
F532 % Sat. GenePix percentage of feature pixels at wavelength 532 that are saturated
Ratio of Medians (635/532) GenePix ratio of the median intensities of each feature for wavelengths 635 and 532, with the median background intensity subtracted
Ratio of Means (635/532) GenePix ratio of the arithmetic mean intensities of each feature for wavelengths 635 and 532, with the median background intensity subtracted
Mean of Ratios (635/532) GenePix geometric mean of the pixel-by-pixel ratios of pixel intensities for wavelengths 635 and 532, with the median background intensity subtracted
Ratios SD (635/532) GenePix standard deviation of the log of pixel intensity ratios for wavelengths 635 and 532
Rgn Ratio (635/532) GenePix regression ratio for wavelengths 635 and 532 (slope of the line of best fit (chi-square or minimum-of-squares method) through the set of pixels in a circle of diameter twice that of the feature-indicator of the current feature)
F Pixels GenePix total number of feature pixels
B Pixels GenePix total number of local background pixels
Sum of Medians GenePix sum of the median intensities for each wavelength, with the median background intensity at each wavelength subtracted
Sum of Means GenePix sum of the arithmetic mean intensities for each wavelength, with the median background intensity at each wavelength subtracted
Log Ratio (635/532) GenePix log2 transform of the ratio of the medians for wavelengths 635 and 532
F635 Median - B635 GenePix median feature pixel intensity at wavelength 635 with the median background intensity subtracted
F532 Median - B532 GenePix median feature pixel intensity at wavelength 532 with the median background intensity subtracted
F635 Mean - B635 GenePix mean feature pixel intensity at wavelength 635 with the median background intensity subtracted
F532 Mean - B532 GenePix mean feature pixel intensity at wavelength 635 with the median background intensity subtracted

Data table
ID_REF PRE_VALUE VALUE Median of Ratios (635/532) Rgn R^2 (635/532) GenePix Flags 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 (635/532) Ratio of Means (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532
15S_rRNA1 1.65298737 0.7251 0.821 0.975 0 110 4350 4616 2914 179 218 294 97 91 0 5783 5832 3796 351 398 384 88 85 0 0.768 0.81 0.956 1.675 0.787 80 512 9603 9918 -0.381 4171 5432 4437 5481
15S_rRNA2 1.812044621 0.8576 0.9 0.952 0 110 10538 13624 7933 191 207 104 100 100 0 10646 15089 8882 358 378 101 100 100 0 1.006 0.912 0.916 1.259 0.903 80 513 20635 28164 0.008 10347 10288 13433 14731
21S_rRNA0 1.713388858 0.7769 0.851 0.95 0 110 5388 6646 3162 205 215 59 100 100 0 6438 7869 3816 389 395 68 100 100 0 0.857 0.861 0.868 1.215 0.85 80 539 11232 13921 -0.223 5183 6049 6441 7480
21S_rRNA1 1.538224545 0.6213 0.764 0.953 0 100 4428 5376 3410 182 188 37 100 100 0 6220 7386 4786 363 368 47 100 98 0 0.725 0.74 0.8 1.399 0.719 80 430 10103 12217 -0.464 4246 5857 5194 7023
21S_rRNA2 1.70130856 0.7666 0.845 0.977 0 120 9080 10140 7082 184 191 53 100 100 0 11586 12479 8757 356 364 62 95 95 0 0.792 0.821 0.885 1.384 0.816 120 514 20126 22079 -0.336 8896 11230 9956 12123
9S_rRNA 1.506010418 0.5907 0.748 0.887 0 100 1696 2223 1471 196 202 47 100 100 0 2378 3110 1983 366 375 58 100 100 0 0.746 0.739 0.745 1.361 0.725 80 498 3512 4771 -0.424 1500 2012 2027 2744
CEN1 1.713388858 0.7769 0.851 0.925 0 120 1785 1954 514 210 214 45 100 100 0 2321 2414 666 371 375 50 100 100 0 0.808 0.854 0.866 1.271 0.839 120 566 3525 3787 -0.308 1575 1950 1744 2043
CEN10 1.892579937 0.9204 0.94 0.906 0 120 1740 1673 520 216 236 81 100 100 0 2068 2032 582 438 459 98 99 99 0 0.935 0.914 0.93 1.367 0.904 120 621 3154 3051 -0.097 1524 1630 1457 1594
CEN11 0.86 0.892 -50 150 532 808 675 206 214 60 61 54 0 710 1159 891 396 406 71 58 54 0 1.038 0.789 0.843 2.39 0.755 156 840 640 1365 0.054 326 314 602 763
CEN12 1.659027519 0.7303 0.824 0.954 0 120 1887 1829 409 197 208 62 100 100 0 2438 2385 559 406 413 59 100 100 0 0.832 0.825 0.836 1.24 0.81 120 613 3722 3611 -0.266 1690 2032 1632 1979
CEN13 1.733522687 0.7937 0.861 0.968 0 90 1905 1872 655 204 217 66 100 100 0 2461 2338 785 404 415 75 98 98 0 0.827 0.862 0.856 1.184 0.858 52 383 3758 3602 -0.274 1701 2057 1668 1934
CEN14 1.648960605 0.7216 0.819 0.897 0 130 1843 1745 554 205 212 48 99 99 0 2343 2250 708 387 395 76 99 97 0 0.837 0.827 0.838 1.498 0.798 120 531 3594 3403 -0.256 1638 1956 1540 1863
CEN15 0.602 0.726 -50 150 247 325 210 206 216 63 46 35 0 459 576 268 401 416 88 44 37 0 0.707 0.68 0.677 2.403 0.738 156 840 99 294 -0.5 41 58 119 175
CEN16 1.63889369 0.7127 0.814 0.912 0 90 935 1060 430 374 392 107 98 92 0 1306 1377 546 497 518 129 94 88 0 0.693 0.78 0.778 1.299 0.78 52 381 1370 1566 -0.528 561 809 686 880
CEN2 1.803991089 0.8512 0.896 0.922 0 110 2172 2121 449 217 225 56 100 100 0 2629 2516 593 384 394 66 100 100 0 0.871 0.893 0.908 1.258 0.866 80 500 4200 4036 -0.2 1955 2245 1904 2132
CEN3 0.794 0.738 -50 150 397 546 490 226 238 65 68 58 0 598 814 636 406 417 70 65 54 0 0.891 0.784 0.829 2.458 0.748 156 718 363 728 -0.167 171 192 320 408
CEN4 1.727482538 0.7887 0.858 0.816 0 100 1901 1718 585 230 426 1984 21 0 0 2369 2189 780 414 706 2329 20 0 0 0.855 0.838 0.916 1.879 0.809 80 537 3626 3263 -0.226 1671 1955 1488 1775
CEN5 1.697281795 0.7632 0.843 0.944 0 130 1715 1716 558 198 209 73 100 100 0 2310 2264 730 410 423 101 99 99 0 0.798 0.819 0.855 1.347 0.812 120 568 3417 3372 -0.325 1517 1900 1518 1854
CEN6 1.830165067 0.8720 0.909 0.953 0 120 2238 2097 723 202 215 65 100 100 0 2675 2509 899 405 426 132 98 95 0 0.897 0.901 0.954 1.341 0.872 120 551 4306 3999 -0.157 2036 2270 1895 2104
CEN7 0.871 0.943 -50 150 779 925 723 207 450 1471 15 0 0 1050 1249 864 391 585 1231 31 6 0 0.868 0.837 0.859 2.264 0.832 156 835 1231 1576 -0.204 572 659 718 858

Total number of rows: 13173

Table truncated, full table size 2457 Kbytes.




Supplementary data files not provided
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