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Sample GSM95355 Query DataSets for GSM95355
Status Public on Mar 17, 2006
Title A364a_S_phase_LiUP1_202_RME7-21_wtrerep_135mN1_35
Sample type genomic
 
Channel 1
Source name S phase DNA A364a
Organism Saccharomyces cerevisiae
Characteristics YJL5834 135 minutes after release from G1 (alpha factor) into 0.1M hydroxyurea
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 A364a
Organism Saccharomyces cerevisiae
Characteristics YJL5834 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 1D 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 1.35C.
 
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 0.616 0.266 -50 100 528 619 293 456 456 49 62 40 0 537 777 604 438 437 41 68 56 0 0.727 0.481 0.639 3.351 0.308 80 512 171 502 -0.459 72 99 163 339
15S_rRNA1 0.807 0.1 -50 100 579 599 201 543 543 52 45 32 0 575 602 196 533 534 49 43 31 0 0.857 0.812 0.978 3.261 0.865 80 500 78 125 -0.222 36 42 56 69
15S_rRNA2 0.917 0.388 -50 100 735 792 267 669 668 55 53 27 0 672 813 387 589 591 48 65 46 0 0.795 0.549 0.905 3.731 0.564 80 465 149 347 -0.331 66 83 123 224
21S_rRNA_3 0.573 0.675 -100 60 1019 1043 353 529 533 54 93 87 0 1450 1445 461 550 557 61 96 96 0 0.544 0.574 0.545 1.815 0.595 32 176 1390 1409 -0.877 490 900 514 895
21S_rRNA_4 0.840916132 -0.2500 0.554 0.622 0 100 1744 1887 942 703 710 69 96 90 0 2619 2666 1216 675 680 57 97 97 0 0.535 0.595 0.539 2.349 0.601 80 485 2985 3175 -0.901 1041 1944 1184 1991
21S_rRNA0 0.925918485 -0.1110 0.61 0.679 0 120 4197 4281 1846 473 481 84 100 99 0 6829 6995 3560 495 505 136 94 92 0 0.588 0.586 0.54 2.648 0.51 120 677 10058 10308 -0.766 3724 6334 3808 6500
21S_rRNA1 0.708 0.11 -50 100 669 722 223 575 575 52 58 48 0 707 803 369 547 551 55 70 61 0 0.587 0.574 0.706 3.431 0.305 80 541 254 403 -0.767 94 160 147 256
21S_rRNA2 0.874309914 -0.1938 0.576 0.523 0 80 2827 2933 1538 604 612 65 100 100 0 4502 4449 2528 612 615 53 100 100 0 0.571 0.607 0.588 2.13 0.518 52 340 6113 6166 -0.807 2223 3890 2329 3837
9S_rRNA 0.773 0.201 -50 100 709 759 218 619 626 68 57 33 0 734 800 207 608 615 64 75 48 0 0.714 0.729 0.679 3.146 0.889 80 502 216 332 -0.485 90 126 140 192
9S_rRNA_5 0.511 0.225 -50 100 601 618 137 518 521 68 57 36 0 649 722 244 476 480 73 67 56 0 0.48 0.407 0.554 2.658 0.542 80 535 256 346 -1.06 83 173 100 246
CEN1 0.804 0.277 -100 70 790 927 301 526 578 151 84 43 0 799 872 249 513 568 159 87 43 0 0.923 1.117 1.007 2.049 1.093 32 235 550 760 -0.115 264 286 401 359
CEN10 0.846 0.017 -50 100 540 543 78 547 554 75 11 3 0 568 582 81 522 524 50 47 30 0 -0.152 -0.067 0.842 3.984 0.614 80 506 39 56 Error -7 46 -4 60
CEN11 1.119 0.022 -50 100 672 634 170 711 720 82 6 0 0 693 654 154 663 671 85 23 0 0 -1.3 8.556 1.015 4.868 1.882 80 523 -9 -86 Error -39 30 -77 -9
CEN12 0.605 0.224 -50 100 644 597 149 549 556 64 56 35 0 744 720 172 577 583 69 77 57 0 0.569 0.336 0.531 2.85 0.585 80 514 262 191 -0.814 95 167 48 143
CEN13 0.769 0.236 -50 100 819 891 405 607 607 53 68 63 0 875 942 443 611 615 47 76 67 0 0.803 0.858 0.757 2.568 0.795 80 497 476 615 -0.316 212 264 284 331
CEN14 0.709 0.085 -50 100 701 688 191 595 599 69 65 40 0 820 831 363 609 612 59 78 66 0 0.502 0.419 0.62 2.972 0.292 80 489 317 315 -0.993 106 211 93 222
CEN15 0.873 0.309 -50 100 616 577 177 639 646 72 20 5 0 723 685 195 652 660 64 53 31 0 -0.324 -1.879 0.924 3.66 0.88 80 480 48 -29 Error -23 71 -62 33
CEN16 0.703 0.085 -50 100 547 542 115 551 550 49 23 11 0 566 564 128 517 517 43 51 35 0 -0.082 -0.191 0.761 4.197 0.8 80 508 45 38 Error -4 49 -9 47
CEN2 0.828 0.347 -50 100 653 632 221 516 528 99 56 32 0 674 669 199 528 548 104 58 46 0 0.938 0.823 0.948 2.88 1.098 80 498 283 257 -0.092 137 146 116 141
CEN3 0.881 0.316 -50 100 472 459 142 443 458 105 15 3 0 533 517 133 457 462 66 56 21 0 0.382 0.267 0.786 2.985 0.977 80 527 105 76 -1.39 29 76 16 60

Total number of rows: 14062

Table truncated, full table size 2440 Kbytes.




Supplementary data files not provided

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