NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM95353 Query DataSets for GSM95353
Status Public on Mar 17, 2006
Title A364a_S_phase_LiUP1_062_RME7-26_wtrerep_135minN1_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 1.179 0.687 -100 50 2362 3671 2995 218 243 110 100 100 0 2152 2792 1674 259 315 213 100 100 0 1.133 1.363 1.027 2.798 1.4 12 104 4037 5986 0.18 2144 1893 3453 2533
15S_rRNA1 1.527905199 0.6116 1.168 0.695 0 90 1566 1957 1237 244 247 49 100 98 0 1783 1791 935 268 275 55 98 98 0 0.873 1.125 1.034 1.932 1.274 52 411 2837 3236 -0.197 1322 1515 1713 1523
15S_rRNA2 0.518 0.673 -100 50 3270 3882 2740 204 277 210 100 91 0 6790 6958 2989 246 325 171 100 100 0 0.469 0.548 0.421 2.143 0.666 12 104 9610 10390 -1.094 3066 6544 3678 6712
21S_rRNA_3 0.732 0.644 -100 60 2028 2320 1504 187 189 35 100 96 0 2687 3179 2358 222 222 28 100 100 0 0.747 0.721 0.678 1.806 0.714 32 176 4306 5090 -0.421 1841 2465 2133 2957
21S_rRNA_4 0.806 0.609 -100 80 2209 2756 1899 197 223 107 100 100 0 3485 4315 3414 246 293 179 100 100 0 0.621 0.629 0.707 2.282 0.521 52 340 5251 6628 -0.687 2012 3239 2559 4069
21S_rRNA0 0.902615229 -0.1478 0.69 0.856 0 110 12328 12671 5423 212 217 59 100 100 0 18408 18569 7929 249 260 130 100 98 0 0.667 0.68 0.702 1.945 0.66 80 583 30275 30779 -0.584 12116 18159 12459 18320
21S_rRNA1 0.754 0.648 -100 80 3243 3225 1744 257 262 54 100 100 0 3611 3885 1803 287 293 42 100 100 0 0.898 0.825 0.708 2.552 0.838 52 340 6310 6566 -0.155 2986 3324 2968 3598
21S_rRNA2 0.850289708 -0.2340 0.65 0.757 0 80 8580 9234 6960 224 233 54 100 100 0 13602 15016 10246 276 296 153 100 100 0 0.627 0.611 0.564 2.303 0.601 52 340 21682 23750 -0.673 8356 13326 9010 14740
9S_rRNA 1.007 0.607 -100 70 1139 1649 1278 261 309 297 71 59 0 1497 1794 1291 312 328 162 87 78 0 0.741 0.937 0.856 2.983 1.028 32 236 2063 2870 -0.433 878 1185 1388 1482
9S_rRNA_5 1.129 0.681 -100 90 1653 2361 1862 251 268 168 100 100 0 1671 1843 944 281 293 93 100 100 0 1.009 1.351 1.201 1.764 1.85 52 420 2792 3672 0.012 1402 1390 2110 1562
CEN1 1.597236514 0.6756 1.221 0.813 0 120 2594 2526 1003 228 233 45 100 100 0 2069 2158 792 259 262 36 100 100 0 1.307 1.21 1.17 1.682 1.253 120 525 4176 4197 0.386 2366 1810 2298 1899
CEN10 1.109 0.568 -100 70 1065 1701 1332 236 258 122 93 93 0 1283 1610 1011 266 282 96 100 100 0 0.815 1.09 0.921 2.919 1.254 32 236 1846 2809 -0.295 829 1017 1465 1344
CEN11 1.061 0.326 -100 50 1005 1126 414 231 279 175 100 91 0 1003 1151 417 281 334 190 100 91 0 1.072 1.029 1.03 1.884 0.838 12 104 1496 1765 0.1 774 722 895 870
CEN12 0.877 0.551 -100 50 634 739 362 205 316 246 83 50 0 717 716 306 243 375 266 66 50 0 0.905 1.129 1.142 2.092 1.125 12 104 903 1007 -0.144 429 474 534 473
CEN13 0.975 0.565 -100 60 1657 1954 1358 197 214 100 96 93 0 1670 1911 1168 254 258 46 100 100 0 1.031 1.06 0.981 2.792 1.187 32 176 2876 3414 0.044 1460 1416 1757 1657
CEN14 1.153 0.624 -100 60 1187 1313 752 208 217 79 100 96 0 1189 1267 738 259 266 66 93 93 0 1.053 1.096 1.239 2.369 0.962 32 176 1909 2113 0.074 979 930 1105 1008
CEN15 0.897 0.517 -100 60 924 945 331 197 200 43 100 100 0 1006 1106 428 244 248 36 100 96 0 0.954 0.868 0.892 1.809 0.811 32 176 1489 1610 -0.068 727 762 748 862
CEN16 1.157 0.568 -100 70 1276 1462 816 236 264 145 96 90 0 1271 1414 684 269 293 123 100 100 0 1.038 1.071 0.94 2.329 1.351 32 236 2042 2371 0.054 1040 1002 1226 1145
CEN2 1.228 0.695 -100 90 1099 1208 672 213 228 83 96 96 0 951 1045 440 252 275 118 96 94 0 1.268 1.255 1.256 1.686 1.321 52 372 1585 1788 0.342 886 699 995 793
CEN3 0.847 0.772 -100 80 934 939 370 201 206 36 98 96 0 997 1048 340 243 249 42 100 100 0 0.972 0.917 0.87 1.725 0.946 52 340 1487 1543 -0.041 733 754 738 805

Total number of rows: 14062

Table truncated, full table size 2562 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap