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Sample GSM95360 Query DataSets for GSM95360
Status Public on Mar 17, 2006
Title OMC_S_Rerep_LiUP1_084_RME7-11_G1_vs_0_1MHU_OMC_rerepN1_40
Sample type genomic
 
Channel 1
Source name S phase re-replicating DNA OMC
Organism Saccharomyces cerevisiae
Characteristics YJL3249 240 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea in the presence of galactose
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 phase DNA OMC
Organism Saccharomyces cerevisiae
Characteristics YJL3249 arrested in G1 (alpha factor)
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 3B 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 1.40C.
 
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 1.213259178 0.2789 0.884 0.954 0 50 2022 2016 807 381 406 104 100 100 0 2251 2355 932 433 465 123 100 100 0 0.903 0.851 0.868 1.342 0.832 12 104 3459 3557 -0.148 1641 1818 1635 1922
15S_rRNA1 0.949 0.947 -50 100 756 897 578 340 344 44 85 78 0 799 981 706 391 394 38 83 80 0 1.02 0.944 0.954 1.607 0.862 80 501 824 1147 0.028 416 408 557 590
15S_rRNA2 0.913 0.98 -50 100 703 1721 2107 378 381 49 96 90 0 781 1951 2439 432 436 54 97 92 0 0.931 0.884 0.907 1.606 0.869 80 450 674 2862 -0.103 325 349 1343 1519
21S_rRNA_3 1.038956106 0.0551 0.757 0.956 0 50 1730 1814 681 352 382 112 100 100 0 2548 2409 929 397 437 135 100 100 0 0.641 0.727 0.739 1.126 0.759 12 104 3529 3474 -0.642 1378 2151 1462 2012
21S_rRNA_4 1.209141783 0.2740 0.881 0.986 0 70 3000 4643 3528 393 472 271 96 96 0 3637 5457 4198 477 577 304 96 96 0 0.825 0.853 0.868 1.232 0.857 32 236 5767 9230 -0.278 2607 3160 4250 4980
21S_rRNA0 1.110324293 0.1510 0.809 0.994 0 110 9598 10688 5299 366 413 386 97 97 0 11755 13108 6650 428 498 536 98 97 0 0.815 0.814 0.809 1.133 0.805 80 580 20559 23002 -0.295 9232 11327 10322 12680
21S_rRNA1 1.167967829 0.2240 0.851 0.976 0 70 2997 3434 1893 368 390 149 100 100 0 3490 4011 2243 436 474 228 100 96 0 0.861 0.858 0.872 1.198 0.84 32 236 5683 6641 -0.216 2629 3054 3066 3575
21S_rRNA2 1.196789597 0.2592 0.872 0.982 0 80 9728 11509 7832 386 387 41 100 100 0 11813 12876 9079 423 426 44 100 100 0 0.82 0.893 0.909 1.26 0.881 52 340 20732 23576 -0.286 9342 11390 11123 12453
9S_rRNA 0.694 0.868 -50 100 495 673 506 357 352 220 41 27 0 620 821 647 439 397 255 45 28 0 0.762 0.827 0.724 2.56 0.765 80 499 319 698 -0.391 138 181 316 382
9S_rRNA_5 1.038956106 0.0551 0.757 0.985 0 70 2909 3384 1860 438 454 103 100 100 0 3742 4356 2507 474 499 101 100 100 0 0.756 0.759 0.764 1.148 0.753 32 236 5739 6828 -0.403 2471 3268 2946 3882
CEN1 1.443833321 0.5299 1.052 0.968 0 130 1910 2150 915 353 396 383 99 94 0 1874 2146 901 440 477 380 98 89 0 1.086 1.053 1.076 1.243 1.045 120 580 2991 3503 0.119 1557 1434 1797 1706
CEN10 1.002 0.923 -100 70 1225 1282 488 415 418 54 100 100 0 1289 1356 428 453 457 48 100 100 0 0.969 0.96 0.922 1.351 1.022 32 236 1646 1770 -0.046 810 836 867 903
CEN11 1.001 0.951 -100 50 1414 1629 777 381 583 564 83 41 0 1535 1638 637 434 638 536 83 50 0 0.938 1.037 0.995 1.246 1.061 12 104 2134 2452 -0.092 1033 1101 1248 1204
CEN12 1.047 0.969 -100 70 1075 1226 870 366 425 305 65 50 0 988 1232 840 406 475 332 62 50 0 1.218 1.041 1.205 1.863 1.029 32 236 1291 1686 0.285 709 582 860 826
CEN13 1.589314625 0.6684 1.158 0.919 0 70 1838 2156 1266 366 382 97 90 90 0 1632 1902 1091 436 458 127 90 90 0 1.231 1.221 1.098 2.082 1.205 32 236 2668 3256 0.3 1472 1196 1790 1466
CEN14 1.538533415 0.6216 1.121 0.922 0 50 1755 2131 1109 394 530 422 100 75 0 1959 2017 873 484 625 408 91 83 0 0.923 1.133 1.124 1.282 1.151 12 104 2836 3270 -0.116 1361 1475 1737 1533
CEN15 0.667 0.931 -100 70 871 1061 613 384 391 65 84 81 0 1207 1423 775 450 468 85 90 87 0 0.643 0.696 0.673 1.619 0.743 32 236 1244 1650 -0.636 487 757 677 973
CEN16 0.907 0.934 -100 70 1270 1253 478 385 446 655 62 12 0 1382 1379 468 417 427 68 100 100 0 0.917 0.902 0.862 1.287 0.918 32 236 1850 1830 -0.125 885 965 868 962
CEN2 1.522063833 0.6060 1.109 0.972 0 70 2006 1954 958 357 413 194 100 87 0 1861 1846 812 412 463 187 93 93 0 1.138 1.114 1.108 1.377 1.14 32 236 3098 3031 0.187 1649 1449 1597 1434
CEN3 0.703 0.95 -50 100 513 622 370 365 393 134 51 41 0 647 788 481 414 456 183 53 43 0 0.635 0.687 0.72 1.804 0.76 80 546 381 631 -0.655 148 233 257 374

Total number of rows: 14062

Table truncated, full table size 2573 Kbytes.




Supplementary data files not provided
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