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Sample GSM362938 Query DataSets for GSM362938
Status Public on Jan 28, 2009
Title ChIP Input cell cycle CCTS, 10 min, array replicate 1 | array na_22_64
Sample type genomic
 
Channel 1
Source Name ChIP Input pool
Organism(s) Saccharomyces cerevisiae
Characteristics Strain: BY4741 cdc28(ts)
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.
Label Cy3
Label protocol The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.
 
Channel 2
Source Name 10 min
Organism(s) Saccharomyces cerevisiae
Characteristics Strain: BY4741 cdc28(ts)
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.
Label Cy5
Label protocol The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.
 
 
Hybridization protocol Amplified, labeled ChIP DNA were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.
Description BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours. To release from arrest, cold YPD media was added to shift back to 22C. Cells were harvested after 10 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated. Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input). As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool. The ChIP input and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.
Data processing After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy5/Cy3) were calculated to produce the values given in the data table.
 
Submission date Jan 22, 2009
Contact name Oliver Rando
E-mail(s) Oliver.Rando@umassmed.edu
Phone 508-856-8879
Fax 1-508-856-6464
Organization name UMass Medical School
Street address 364 Plantation St.
City Worcester
State/province MA
ZIP/Postal code 01605-4321
Country USA
 
Platform ID GPL2625
Series (1)
GSE14565 Lack of epigenetic maintenance of active chromatin states in budding yeast

Data table header descriptions
ID_REF Probe ID
Block printing block
VALUE Block Normalized Log2 Ratio (635/532)
Raw Log Ratio (635/532) Raw log (base 2) transform of the ratio (635/532) of the medians, as calculated by GenePix
Diameter diameter in microns of the array feature
F635 Median median feature pixel intensity at wavelength 635 nm
F635 Mean mean feature pixel intensity at wavelength 635 nm
F635 SD standard deviation of the feature pixel intensity at wavelength 635 nm
F635 CV the coefficient of variation of the feature pixel intensity at wavelength 635 nm
B635 the background value that is used for any background subtraction at wavelength 635 nm, determined from local feature background median at wavelength 635 nm
B635 Median median feature pixel background intensity at wavelength 635 nm
B635 Mean mean feature pixel background intensity at wavelength 635 nm
B635 SD standard deviation of the background feature pixel intensity at wavelength 635 nm
B635 CV the coefficient of variation of the local background intensity at wavelength 635 nm
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 635 nm
F635 % Sat. the percentage of feature pixels at wavelength 635 nm that are saturated
F532 Median median feature pixel intensity at wavelength 532 nm
F532 Mean mean feature pixel intensity at wavelength 532 nm
F532 SD standard deviation of the feature pixel intensity at wavelength 532 nm
F532 CV the coefficient of variation of the feature pixel intensity at wavelength 532 nm
B532 the background value that is used for any background subtraction at wavelength 532 nm, determined from local feature background median at wavelength 532 nm
B532 Median median feature pixel background intensity at wavelength 532 nm
B532 Mean mean feature pixel background intensity at wavelength 532 nm
B532 SD standard deviation of the background feature pixel intensity at wavelength 532 nm
B532 CV the coefficient of variation of the local background intensity at wavelength 532 nm
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm
F532 % Sat. the percentage of feature pixels at wavelength 532 nm that are saturated
Ratio of Medians (635/532) the ratio (635/532) of the median intensities of each feature for each wavelength, with the median background subtracted
Ratio of Means (635/532) the ratio (635/532) of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted
Median of Ratios (635/532) the median of pixel-by-pixel ratios (635/532) of pixel intensities, with the median background subtracted
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios (635/532) of pixel intensities, with the median background subtracted
Ratios SD (635/532) the geometric standard deviation of the pixel intensity ratios
Rgn Ratio (635/532) the regression ratio (635/532) of every pixel in a 2-feature-diameter circle around the center of the feature
Rgn R2 (635/532) the coefficient of determination for the current regression value
F Pixels the total number of feature pixels
B Pixels the total number of background pixels
Circularity a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular
Sum of Medians (635/532) the sum of the median intensities for each wavelength, with the median background subtracted
Sum of Means (635/532) the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted
F635 Median - B635 the median feature pixel intensity at wavelength 635 nm with the median background subtracted
F532 Median - B532 the median feature pixel intensity at wavelength 532 nm with the median background subtracted
F635 Mean - B635 the mean feature pixel intensity at wavelength 635 nm with the median background subtracted
F532 Mean - B532 the mean feature pixel intensity at wavelength 532 nm with the median background subtracted
F635 Total Intensity the sum of feature pixel intensities at wavelength 635 nm
F532 Total Intensity the sum of feature pixel intensities at wavelength 532 nm
SNR 635 the signal-to-noise ratio at wavelength 635 nm, defined by (Mean Foreground 635- Mean Background 635) / (Standard deviation of Background 635)
SNR 532 the signal-to-noise ratio at wavelength 532 nm, defined by (Mean Foreground 532- Mean Background 532) / (Standard deviation of Background 532)
Flags the type of flag associated with a feature; 100 = good, bad = -100, not found = -50, absent = -75, unflagged = 0
Autoflag flag used to mark whether or not a good or bad flag was applied via a number of criteria defined in boolean terms; 1 = flagged, 0 = not flagged

Data table
ID_REF Block VALUE Raw Log Ratio (635/532) Diameter F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Autoflag
493550 45 0.653760544 0.194 110 4723 5200 2438 46 435 435 462 249 53 100 99 0 4218 4808 2177 45 469 469 484 174 35 100 100 0 1.144 1.098 1.076 1.094 1.758 1.113 0.806 414 2486 94 8037 9104 4288 3749 4765 4339 2152840 1990504 19.028 24.851 0 0
493552 37 0.352402674 0.046 120 6774 7265 3349 46 395 395 425 241 56 100 100 0 6610 7154 3248 45 433 433 453 176 38 100 100 0 1.033 1.022 0.998 1.018 1.347 1.026 0.929 471 2901 96 12556 13591 6379 6177 6870 6721 3421730 3369320 28.382 38.074 0 0
493554 29 0.273266392 0.209 125 7294 7127 2114 29 373 373 398 227 57 100 100 0 6386 6190 2062 33 398 398 409 147 35 99 98 0 1.156 1.166 1.175 1.220 1.432 1.147 0.921 551 2879 95 12909 12546 6921 5988 6754 5792 3927184 3410874 29.643 39.327 0 0
493556 21 0.284010049 0.284 140 7941 7916 3032 38 357 357 394 234 59 100 100 0 6612 6706 2659 39 384 384 406 175 43 99 99 0 1.218 1.196 1.197 1.225 1.420 1.191 0.924 635 3489 95 13812 13881 7584 6228 7559 6322 5026900 4258170 32.145 36.000 0 0
493558 13 0.107286218 0.105 155 10837 10714 3180 29 359 359 392 218 55 100 100 0 10116 9845 2989 30 372 372 388 144 37 100 100 0 1.075 1.093 1.085 1.108 1.348 1.087 0.932 775 3920 96 20222 19828 10478 9744 10355 9473 8303142 7630133 47.349 65.674 0 0
493560 5 0.231088895 0.247 120 9319 9569 3324 34 382 382 409 231 56 100 100 0 7915 7746 2796 36 384 384 398 147 36 100 99 0 1.187 1.248 1.245 1.285 1.371 1.241 0.937 467 2822 96 16468 16549 8937 7531 9187 7362 4468774 3617597 39.654 49.986 0 0
493562 45 0.037405611 -0.517 125 4208 4194 1440 34 441 441 470 251 53 99 98 0 5863 5710 1830 32 471 471 487 172 35 98 98 0 0.699 0.716 0.699 0.697 1.783 0.705 0.824 514 2813 95 9159 8992 3767 5392 3753 5239 2155851 2934901 14.837 30.366 0 0
493564 37 0.286414385 -0.079 140 3816 3918 1540 39 393 393 424 244 57 99 98 0 4055 4049 1497 36 439 439 457 174 38 99 98 0 0.947 0.976 0.964 0.987 1.709 0.986 0.843 627 3247 94 7039 7135 3423 3616 3525 3610 2456872 2538737 14.320 20.644 0 0
493566 29 0.136827088 0.015 140 2265 2416 969 40 379 379 407 242 59 99 99 0 2278 2332 895 38 412 412 430 182 42 97 95 0 1.011 1.061 0.972 1.073 2.046 1.096 0.591 586 3109 97 3752 3957 1886 1866 2037 1920 1415727 1366494 8.302 10.451 0 0
493568 21 0.11301298 0.058 160 2911 2895 1050 36 377 377 414 248 59 98 97 0 2835 2772 983 35 401 401 425 185 43 96 95 0 1.041 1.062 1.042 1.054 1.553 1.072 0.807 756 3402 95 4968 4889 2534 2434 2518 2371 2188688 2095355 10.004 12.686 0 0
493570 13 -0.218323397 -0.214 135 1917 2005 772 38 378 378 409 233 56 99 95 0 2177 2257 911 40 392 392 409 153 37 98 96 0 0.862 0.872 0.838 0.897 2.091 0.846 0.659 558 2619 75 3324 3492 1539 1785 1627 1865 1118815 1259571 6.850 12.078 0 0
493572 5 -0.370624132 -0.293 120 2265 2293 801 34 382 382 407 229 56 99 97 0 2697 2713 990 36 390 390 401 146 36 96 96 0 0.816 0.823 0.812 0.827 1.750 0.805 0.769 514 2489 93 4190 4234 1883 2307 1911 2323 1178488 1394589 8.236 15.836 0 0
493574 47 -0.066727613 -0.389 105 1376 1441 515 35 446 446 479 248 51 94 83 0 1718 1739 469 26 500 500 513 171 33 99 98 0 0.764 0.803 0.786 0.749 2.227 0.863 0.452 330 2243 91 2148 2234 930 1218 995 1239 475500 573713 3.879 7.170 0 0
493576 39 -0.259261597 -0.388 120 1309 1364 471 34 448 448 476 254 53 93 80 0 1609 1631 441 27 482 482 498 173 34 99 98 0 0.764 0.797 0.809 0.748 2.201 0.861 0.450 404 2871 83 1988 2065 861 1127 916 1149 550929 658747 3.496 6.549 0 0
493578 31 -0.300501336 -0.371 135 1351 1399 499 35 437 437 464 245 52 93 82 0 1664 1664 512 30 482 482 492 166 33 97 95 0 0.773 0.814 0.841 0.777 2.311 0.853 0.511 592 2971 97 2096 2144 914 1182 962 1182 828224 985184 3.816 7.060 0 0
493580 23 -0.039142351 -0.071 85 11443 11470 3989 34 405 405 435 239 54 100 99 0 12018 11650 4232 36 425 425 436 155 35 100 100 0 0.952 0.986 0.951 0.999 1.666 0.974 0.916 260 1533 86 22631 22290 11038 11593 11065 11225 2982112 3028999 46.172 72.348 0 0
493582 15 0.111255142 0.148 125 8860 9570 4751 49 413 413 443 244 55 100 100 0 8067 8737 4398 50 445 445 456 159 34 98 98 0 1.108 1.104 1.105 1.146 1.573 1.098 0.917 588 2609 92 16069 17449 8447 7622 9157 8292 5627432 5137561 37.406 52.082 0 0
493584 7 0.233022083 0.333 130 9213 10340 4813 46 440 440 485 287 59 100 100 0 7421 8348 4048 48 455 455 482 192 39 99 99 0 1.259 1.254 1.242 1.294 1.519 1.247 0.906 620 2565 90 15739 17793 8773 6966 9900 7893 6410525 5175982 34.338 40.969 0 0
493586 47 0.188795141 0.063 90 4938 5142 2172 42 463 463 486 260 53 100 100 0 4772 5368 2325 43 488 488 502 171 34 100 100 0 1.045 0.959 0.980 0.969 1.792 0.948 0.781 293 1778 93 8759 9559 4475 4284 4679 4880 1506471 1572865 17.908 28.456 0 0
493588 39 0.224133065 0.114 125 2251 2265 732 32 441 441 475 252 53 97 96 0 2146 2111 672 31 474 474 489 168 34 97 95 0 1.083 1.114 1.108 1.112 1.689 1.145 0.717 453 2858 77 3482 3461 1810 1672 1824 1637 1026118 956073 7.103 9.655 0 0

Total number of rows: 24864

Table truncated, full table size 5845 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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