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Sample GSM95394 Query DataSets for GSM95394
Status Public on Mar 17, 2006
Title MC2A_cdc7_23_G2_Rerep_LiUP1_073_RME7-9_G2_MC_cdc7-1_rerep23N2_0
Sample type genomic
 
Channel 1
Source name G2 phase re-replicating DNA MC2A cdc7-1
Organism Saccharomyces cerevisiae
Characteristics YJL5822 240 minutes after galactose induction while arrested at G2 phase at 23 degrees C
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 cdc7-1
Organism Saccharomyces cerevisiae
Characteristics YJL5816 240 minutes after galactose induction while arrested at G2 phase at 23 degrees C
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 S13 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_rRNA_2 1.23913624 0.3093 0.565 0.973 0 50 2865 3305 2361 368 461 224 91 83 0 5101 5583 3988 462 604 276 91 91 0 0.538 0.574 0.513 1.391 0.58 12 104 7136 8058 -0.894 2497 4639 2937 5121
15S_rRNA1 0.82 0.878 -100 90 1109 1184 469 370 382 70 96 90 0 1256 1308 565 372 385 67 96 94 0 0.836 0.87 0.876 1.58 0.849 52 412 1623 1750 -0.258 739 884 814 936
15S_rRNA2 1.899277848 0.9255 0.866 0.994 0 90 1650 3213 2647 563 571 81 98 98 0 1661 3445 3104 365 370 49 100 98 0 0.839 0.86 0.845 1.366 0.857 52 383 2383 5730 -0.254 1087 1296 2650 3080
21S_rRNA_3 1.405816514 0.4914 0.641 0.984 0 60 2646 2604 1139 344 353 63 100 100 0 3850 3792 1621 309 351 264 100 96 0 0.65 0.649 0.633 1.15 0.661 32 176 5843 5743 -0.621 2302 3541 2260 3483
21S_rRNA_4 1.923402625 0.9437 0.877 0.995 0 100 5609 8111 6527 570 577 91 100 100 0 6295 8998 7388 382 383 49 100 100 0 0.852 0.875 0.889 1.189 0.879 80 493 10952 16157 -0.231 5039 5913 7541 8616
21S_rRNA0 1.73917706 0.7984 0.793 0.996 0 110 15428 15752 2898 438 671 1516 100 100 0 19549 19745 3703 447 754 2024 100 100 0 0.785 0.794 0.794 1.046 0.784 80 504 34092 34612 -0.35 14990 19102 15314 19298
21S_rRNA1 1.508895103 0.5935 0.688 0.96 0 100 2916 3072 1791 411 438 184 96 92 0 4424 4451 2919 418 449 193 95 91 0 0.625 0.66 0.733 1.598 0.637 80 517 6511 6694 -0.677 2505 4006 2661 4033
21S_rRNA2 1.640484793 0.7141 0.748 0.994 0 90 17759 16350 10181 512 524 115 98 96 0 22637 21649 13694 425 454 148 96 94 0 0.776 0.746 0.778 1.216 0.745 52 411 39459 37062 -0.365 17247 22212 15838 21224
9S_rRNA 1.138 0.808 -100 50 1212 1220 590 519 703 464 75 33 0 1055 1083 469 435 686 667 33 8 0 1.118 1.082 1.285 1.563 0.781 12 104 1313 1349 0.161 693 620 701 648
9S_rRNA_5 1.456259228 0.5423 0.664 0.981 0 70 3627 3766 1715 376 462 226 100 100 0 5316 5495 2886 408 521 275 100 100 0 0.662 0.666 0.711 1.25 0.638 32 236 8159 8477 -0.594 3251 4908 3390 5087
CEN1 1.701893314 0.7671 0.776 0.99 0 130 2623 2502 678 328 330 37 100 100 0 3260 3184 922 373 375 36 100 100 0 0.795 0.773 0.78 1.101 0.766 120 528 5182 4985 -0.331 2295 2887 2174 2811
CEN10 1.772074482 0.8254 0.808 0.847 0 70 1661 1699 351 339 346 85 100 100 0 1941 2033 482 362 397 258 100 100 0 0.837 0.814 0.822 1.112 0.769 32 236 2901 3031 -0.256 1322 1579 1360 1671
CEN11 0.788 0.966 -100 70 1334 1414 310 476 496 118 100 100 0 1424 1558 376 348 369 101 100 100 0 0.797 0.775 0.77 1.127 0.844 32 236 1934 2148 -0.327 858 1076 938 1210
CEN12 0.665 0.98 -100 90 1225 1222 518 368 389 174 90 80 0 1560 1607 729 326 361 234 94 86 0 0.694 0.667 0.645 1.275 0.715 52 403 2091 2135 -0.526 857 1234 854 1281
CEN13 1.84225565 0.8815 0.84 0.976 0 60 2528 2527 809 554 683 536 93 84 0 2756 2704 840 383 555 637 93 87 0 0.832 0.85 0.817 1.213 0.873 32 176 4347 4294 -0.266 1974 2373 1973 2321
CEN14 1.807165066 0.8537 0.824 0.964 0 60 2431 2283 978 600 727 526 87 75 0 2589 2549 1248 422 643 667 87 78 0 0.845 0.791 0.783 1.438 0.803 32 176 3998 3810 -0.243 1831 2167 1683 2127
CEN15 0.617 0.95 -100 80 1252 1161 345 551 546 80 90 88 0 1540 1474 508 435 442 89 92 90 0 0.634 0.587 0.639 2.212 0.649 52 340 1806 1649 -0.657 701 1105 610 1039
CEN16 0.706 0.913 -100 60 1254 1196 299 356 374 100 100 96 0 1604 1565 485 383 409 108 100 100 0 0.735 0.711 0.722 1.168 0.682 32 176 2119 2022 -0.443 898 1221 840 1182
CEN2 1.708472799 0.7727 0.779 0.972 0 110 1874 1718 559 404 441 187 98 92 0 2161 2023 789 357 398 210 100 92 0 0.815 0.789 0.816 1.24 0.779 80 469 3274 2980 -0.295 1470 1804 1314 1666
CEN3 0.828 0.938 -100 80 1053 1078 277 437 451 90 100 100 0 1116 1183 384 395 414 110 100 100 0 0.854 0.813 0.831 1.19 0.758 52 303 1337 1429 -0.227 616 721 641 788

Total number of rows: 14062

Table truncated, full table size 2584 Kbytes.




Supplementary data files not provided
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