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Sample GSM95374 Query DataSets for GSM95374
Status Public on Mar 17, 2006
Title OC_G1_Release_LiUP1_174_RME6-22_G1_Galp_vs_OCrerepN2_60
Sample type genomic
 
Channel 1
Source name G1 release re-replicating DNA OC
Organism Saccharomyces cerevisiae
Characteristics YJL3240 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 O
Organism Saccharomyces cerevisiae
Characteristics YJL4832 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 5E 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 2.60C.
 
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 0.752 0.957 -100 100 993 1451 1600 656 779 735 33 21 0 1302 1911 2014 866 1060 1030 33 17 0 0.773 0.761 0.764 1.442 0.79 80 453 773 1840 -0.372 337 436 795 1045
15S_rRNA1 0.705 0.778 -50 100 895 1034 338 767 780 192 42 25 0 995 1202 532 778 789 152 55 36 0 0.59 0.63 0.699 2.719 0.63 80 467 345 691 -0.762 128 217 267 424
15S_rRNA2 0.769 0.934 -50 100 795 1514 1755 611 624 93 67 50 0 909 1983 2468 682 686 58 82 75 0 0.811 0.694 0.783 2.248 0.701 80 474 411 2204 -0.303 184 227 903 1301
21S_rRNA_3 1.909517341 0.9332 0.684 0.852 0 50 2384 2661 1029 661 823 737 100 58 0 3803 4013 1963 779 1075 1151 91 66 0 0.57 0.618 0.678 1.574 0.621 12 104 4747 5234 -0.812 1723 3024 2000 3234
21S_rRNA_4 1.903933957 0.9290 0.682 0.876 0 90 6942 6854 4648 730 774 267 92 88 0 11103 10119 6804 788 857 340 96 92 0 0.602 0.656 0.663 2.207 0.657 52 366 16527 15455 -0.732 6212 10315 6124 9331
21S_rRNA0 1.884392112 0.9141 0.675 0.973 0 110 11534 11973 3832 609 619 93 100 100 0 17233 17639 5230 707 714 72 100 100 0 0.661 0.671 0.661 1.179 0.675 80 584 27451 28296 -0.597 10925 16526 11364 16932
21S_rRNA1 0.911 0.652 -100 100 81 112 84 62 94 139 11 3 0 68 104 69 57 101 187 7 0 0 1.727 1.064 1.142 3.253 1.229 80 487 30 97 0.788 19 11 50 47
21S_rRNA2 2.082602246 1.0584 0.746 0.952 0 80 11064 11616 7598 686 698 114 100 100 0 14238 16199 10570 739 741 59 100 100 0 0.769 0.707 0.74 1.796 0.702 52 338 23877 26390 -0.379 10378 13499 10930 15460
9S_rRNA 0.674 0.546 -100 100 691 728 230 667 684 101 28 16 0 802 894 403 730 738 91 43 25 0 0.333 0.372 0.727 3.435 0.538 80 540 96 225 -1.585 24 72 61 164
9S_rRNA_5 0.938 0.757 -50 100 65 80 49 60 61 12 28 18 0 59 83 74 56 56 9 36 26 0 1.667 0.741 1.021 3.092 0.755 80 499 8 47 0.737 5 3 20 27
CEN1 0.662 0.931 -100 110 1587 1611 356 678 721 301 95 81 0 2239 2247 468 825 883 616 97 62 0 0.643 0.656 0.608 1.648 0.694 80 508 2323 2355 -0.637 909 1414 933 1422
CEN10 1.115 0.7 -50 100 68 86 51 60 61 11 43 30 0 62 90 82 55 55 9 45 28 0 1.143 0.743 1.379 2.834 0.626 80 488 15 61 0.193 8 7 26 35
CEN11 0.755 0.564 -100 100 800 811 337 647 652 82 57 47 0 1088 1080 459 744 751 63 65 60 0 0.445 0.488 0.76 2.007 0.637 80 534 497 500 -1.169 153 344 164 336
CEN12 2.269645611 1.1825 0.813 0.908 0 90 1591 1470 720 658 662 84 86 80 0 1710 1752 886 763 772 74 82 82 0 0.985 0.821 0.768 1.449 0.816 52 414 1880 1801 -0.021 933 947 812 989
CEN13 2.649315726 1.4056 0.949 0.787 0 50 2039 1990 544 571 807 523 100 75 0 2152 2127 565 672 935 586 91 75 0 0.992 0.975 0.978 1.401 0.947 12 104 2948 2874 -0.012 1468 1480 1419 1455
CEN14 2.336646219 1.2244 0.837 0.815 0 50 1815 1835 276 559 823 600 100 50 0 2157 2212 532 677 963 687 91 58 0 0.849 0.831 0.864 1.27 0.817 12 104 2736 2811 -0.237 1256 1480 1276 1535
CEN15 0.728 0.552 -100 100 853 820 229 684 704 99 68 46 0 1073 1007 293 755 768 131 71 58 0 0.531 0.54 0.697 2.137 0.723 80 523 487 388 -0.912 169 318 136 252
CEN16 0.842 0.346 -100 100 65 75 27 58 59 11 42 31 0 58 76 42 55 56 8 40 28 0 2.333 0.81 0.825 3.276 0.641 80 502 10 38 1.222 7 3 17 21
CEN2 2.10214409 1.0719 0.753 0.919 0 90 1455 1390 456 607 620 101 92 84 0 1700 1757 543 712 725 108 92 92 0 0.858 0.749 0.693 1.587 0.771 52 416 1836 1828 -0.22 848 988 783 1045
CEN3 0.718 0.693 -50 100 730 639 260 563 585 128 53 28 0 922 872 346 701 724 151 56 42 0 0.756 0.444 0.76 2.031 0.738 80 538 388 247 -0.404 167 221 76 171

Total number of rows: 14062

Table truncated, full table size 2502 Kbytes.




Supplementary data files not provided
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