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Sample GSM95388 Query DataSets for GSM95388
Status Public on Mar 17, 2006
Title MC2A_35_G2_Rerep_LiUP1_101_RME7-6_G2_MCrerep35N2_0
Sample type genomic
 
Channel 1
Source name G2 phase re-replicating DNA MC2A
Organism Saccharomyces cerevisiae
Characteristics YJL4489 240 minutes after galactose induction while arrested at G2 phase at 35 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
Organism Saccharomyces cerevisiae
Characteristics YJL4486 240 minutes after galactose induction while arrested at G2 phase at 35 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 7C 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 0.763 0.322 -50 100 342 918 1668 231 264 269 27 18 0 506 2604 5643 417 474 376 28 22 0 1.247 0.314 0.672 3.867 0.138 80 486 200 2874 0.319 111 89 687 2187
15S_rRNA1 0.467 0.065 -100 70 1207 1452 891 265 317 197 96 90 0 3613 7831 12250 434 530 385 84 81 0 0.296 0.16 0.324 3.613 0.034 32 236 4121 8584 -1.755 942 3179 1187 7397
15S_rRNA2 1.238 0.84 -50 100 616 1851 3828 339 350 85 71 67 0 712 1834 3374 440 453 92 70 57 0 1.018 1.085 0.941 2.994 1.021 80 504 549 2906 0.026 277 272 1512 1394
21S_rRNA_3 0.987438605 -0.0182 0.59 0.706 0 60 3865 4196 2110 268 280 80 100 100 0 7793 8744 5209 387 404 109 100 100 0 0.486 0.47 0.482 1.682 0.403 32 176 11003 12285 -1.042 3597 7406 3928 8357
21S_rRNA_4 1.76734774 0.8216 1.056 0.932 0 90 16992 16186 9243 311 500 1411 100 94 0 15961 16769 7892 428 604 1311 100 100 0 1.074 0.971 0.89 1.644 1.025 52 393 32214 32216 0.103 16681 15533 15875 16341
21S_rRNA0 1.715465373 0.7786 1.025 0.972 0 90 39627 38881 7297 302 956 3479 100 100 0 38790 37199 8637 473 1152 3699 100 100 0 1.026 1.05 1.068 1.16 1.022 52 420 77642 75305 0.037 39325 38317 38579 36726
21S_rRNA1 0.634 0.471 -100 70 6752 7349 4297 283 303 98 100 100 0 12451 14317 6540 471 513 322 100 100 0 0.54 0.51 0.448 2.875 0.454 32 236 18449 20912 -0.889 6469 11980 7066 13846
21S_rRNA2 1.66525663 0.7357 0.995 0.884 0 90 23164 24229 14407 304 306 49 100 100 0 26598 26399 11539 478 479 46 100 100 0 0.875 0.923 0.778 2.086 0.995 52 420 48980 49846 -0.192 22860 26120 23925 25921
9S_rRNA 0.157 0.541 -100 50 2827 7553 16275 336 502 428 91 75 0 12623 14322 11955 517 3021 8577 58 25 0 0.206 0.523 0.284 5.584 0.995 12 104 14597 21022 -2.281 2491 12106 7217 13805
9S_rRNA_5 0.651 0.231 -100 80 4158 4220 2509 274 291 83 100 100 0 8261 10167 8064 455 469 84 100 100 0 0.498 0.406 0.421 3 0.175 52 332 11690 13658 -1.007 3884 7806 3946 9712
CEN1 1.8727861 0.9052 1.119 0.897 0 120 2740 2668 745 307 359 145 100 99 0 2764 2598 845 506 535 130 98 97 0 1.078 1.129 1.177 1.398 1.062 120 519 4691 4453 0.108 2433 2258 2361 2092
CEN10 1.073 0.105 -100 80 1443 1440 462 255 261 55 100 100 0 1907 7942 12653 479 490 75 100 100 0 0.832 0.159 0.538 3.924 0.024 52 340 2616 8648 -0.265 1188 1428 1185 7463
CEN11 1.128 0.613 -100 80 1659 1755 783 324 329 59 100 98 0 1642 1740 631 468 470 48 100 100 0 1.137 1.125 1.081 1.362 3.384 52 340 2509 2703 0.185 1335 1174 1431 1272
CEN12 1.772368614 0.8257 1.059 0.901 0 80 1603 1629 794 257 261 41 98 96 0 1513 1692 761 412 420 74 96 94 0 1.223 1.072 1.078 1.787 1.037 52 340 2447 2652 0.29 1346 1101 1372 1280
CEN13 2.097051817 1.0684 1.253 0.919 0 70 2965 3001 956 677 777 533 90 87 0 2430 2475 886 641 714 333 93 87 0 1.279 1.267 1.329 1.297 1.306 32 236 4077 4158 0.355 2288 1789 2324 1834
CEN14 2.011696954 1.0084 1.202 0.945 0 80 2631 2930 1310 652 668 125 98 98 0 2360 2545 1105 626 628 79 98 98 0 1.141 1.187 1.158 1.364 1.19 52 336 3713 4197 0.191 1979 1734 2278 1919
CEN15 0.934 0.625 -100 80 1442 1393 510 407 421 90 96 94 0 1723 1713 659 546 564 94 98 98 0 0.879 0.845 0.822 2.131 0.733 52 340 2212 2153 -0.185 1035 1177 986 1167
CEN16 1.011 0.111 -100 70 1307 1384 512 246 276 112 100 100 0 1628 3239 4224 450 483 314 100 81 0 0.901 0.408 0.692 2.653 0.055 32 236 2239 3927 -0.151 1061 1178 1138 2789
CEN2 1.086 0.272 -100 110 2350 2443 1020 263 266 44 100 100 0 3135 3910 3443 497 498 57 98 98 0 0.791 0.639 0.743 2.647 0.306 80 480 4725 5593 -0.338 2087 2638 2180 3413
CEN3 0.939 0.177 -50 100 752 783 219 292 295 45 100 100 0 1080 1294 956 471 477 95 98 93 0 0.755 0.597 0.743 2.297 0.164 80 506 1069 1314 -0.405 460 609 491 823

Total number of rows: 14062

Table truncated, full table size 2574 Kbytes.




Supplementary data files not provided
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