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Sample GSM95364 Query DataSets for GSM95364
Status Public on Mar 17, 2006
Title OMC_G1_Release_LiU1_173_RME6-22_G1_Galp_vs_OMCrerepN3_20
Sample type genomic
 
Channel 1
Source name G1 release re-replicating DNA OMC
Organism Saccharomyces cerevisiae
Characteristics YJL3248 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest
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 G1 release non-re-replicating DNA OM
Organism Saccharomyces cerevisiae
Characteristics YJL3244 180 minutes after release from G1 (alpha factor) in the presence of galactose into a G2 phase arrest
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 4C 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 3.20C.
 
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_rRNA_2 0.71 0.816 -50 100 79 440 637 405 418 391 20 11 0 76 651 1158 547 501 603 21 7 0 0.692 0.337 0.709 1.461 0.51 80 497 -797 139 -0.531 -326 -471 35 104
15S_rRNA1 0.751 0.729 -50 100 749 874 338 779 797 181 27 18 0 843 1062 518 812 827 174 32 28 0 -0.968 0.38 0.925 3.05 0.672 80 467 1 345 Error -30 31 95 250
15S_rRNA2 2.202517728 1.1392 0.661 0.804 0 60 3490 3777 2152 600 612 92 100 96 0 5391 5486 3086 671 712 117 100 96 0 0.612 0.66 0.659 1.924 0.658 32 176 7610 7992 -0.708 2890 4720 3177 4815
21S_rRNA_3 1.552758338 0.6348 0.466 0.883 0 70 1661 2200 1567 668 671 64 90 87 0 3161 4289 2922 768 777 76 96 96 0 0.415 0.435 0.389 1.892 0.472 32 236 3386 5053 -1.269 993 2393 1532 3521
21S_rRNA_4 1.882636182 0.9128 0.565 0.89 0 80 8909 8161 4240 689 711 134 96 94 0 14451 13362 6933 775 790 113 96 96 0 0.601 0.594 0.57 3.115 0.588 52 333 21896 20059 -0.734 8220 13676 7472 12587
21S_rRNA0 1.952610271 0.9654 0.586 0.933 0 110 11601 11474 3886 731 739 64 100 100 0 20198 19144 7443 799 814 199 97 97 0 0.56 0.586 0.595 1.416 0.563 80 571 30269 29088 -0.836 10870 19399 10743 18345
21S_rRNA1 1.476120051 0.5618 0.443 0.87 0 60 2378 2651 1457 759 788 167 87 84 0 5040 5106 3070 830 879 247 87 87 0 0.385 0.442 0.421 2.534 0.459 32 176 5829 6168 -1.379 1619 4210 1892 4276
21S_rRNA2 2.035912756 1.0257 0.611 0.941 0 80 10460 10692 6179 786 834 175 98 98 0 17325 17723 9992 837 857 112 98 98 0 0.587 0.587 0.554 2.083 0.588 52 339 26162 26792 -0.769 9674 16488 9906 16886
9S_rRNA 0.708 0.668 -100 100 851 965 444 809 846 147 32 22 0 949 1136 631 855 865 82 52 33 0 0.447 0.555 0.876 2.793 0.675 80 531 136 437 -1.162 42 94 156 281
9S_rRNA_5 1 0.976 -100 100 56 65 31 55 906 3819 0 0 0 51 72 94 52 1168 4889 0 0 0 -1 0.5 0.949 2.612 0.693 80 462 0 30 Error 1 -1 10 20
CEN1 2.289152314 1.1948 0.687 0.904 0 100 1405 1360 326 599 600 48 95 95 0 1881 1833 426 686 687 45 97 97 0 0.674 0.663 0.655 1.368 0.67 80 444 2001 1908 -0.568 806 1195 761 1147
CEN10 0.857 0.861 -100 100 998 998 348 727 794 350 42 10 0 1061 1109 394 770 892 707 20 0 0 0.931 0.799 0.95 2.021 0.88 80 520 562 610 -0.103 271 291 271 339
CEN11 1.16 0.771 -50 100 739 816 412 606 622 169 48 40 0 814 871 389 718 743 281 38 16 0 1.385 1.373 1.252 2.491 1.074 80 540 229 363 0.47 133 96 210 153
CEN12 2.365790601 1.2423 0.71 0.799 0 90 1367 1317 610 639 643 61 82 80 0 1870 1814 872 756 760 77 82 82 0 0.654 0.641 0.695 1.601 0.628 52 405 1842 1736 -0.614 728 1114 678 1058
CEN13 3.625324188 1.8581 1.088 0.85 0 60 1825 1856 753 579 708 422 84 78 0 1844 1804 751 686 798 391 90 68 0 1.076 1.142 1.085 1.637 1.046 32 176 2404 2395 0.106 1246 1158 1277 1118
CEN14 2.465753584 1.3020 0.74 0.765 0 60 1552 1539 483 576 684 309 93 81 0 1980 1890 702 682 801 372 87 84 0 0.752 0.797 0.772 1.492 0.755 32 176 2274 2171 -0.411 976 1298 963 1208
CEN15 0.646 0.701 -50 100 882 833 225 727 734 61 63 56 0 1109 1049 312 816 819 65 67 65 0 0.529 0.455 0.655 2.021 0.626 80 518 448 339 -0.919 155 293 106 233
CEN16 0.778 0.723 -50 100 827 862 311 749 748 108 48 43 0 1146 1074 393 788 785 92 61 56 0 0.218 0.395 0.751 2.174 0.706 80 555 436 399 -2.198 78 358 113 286
CEN2 2.655683252 1.4091 0.797 0.954 0 80 1551 1466 553 691 701 97 84 82 0 1843 1744 668 753 771 109 86 86 0 0.789 0.782 0.768 1.436 0.819 52 339 1950 1766 -0.342 860 1090 775 991
CEN3 0.71 0.736 -50 100 890 823 310 718 720 84 65 53 0 1120 1013 353 771 777 97 75 63 0 0.493 0.434 0.792 2.097 0.783 80 523 521 347 -1.021 172 349 105 242

Total number of rows: 14062

Table truncated, full table size 2514 Kbytes.




Supplementary data files not provided
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