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Sample GSM509210 Query DataSets for GSM509210
Status Public on Feb 26, 2010
Title Series 3: H3k4me3 IP from cdc7ts cells 60min after release from arrest in 37C
Sample type other
 
Channel 1
Source name H3K4me3 IP
Organism Saccharomyces cerevisiae
Characteristics strain: CYM36 (cdc7ts)
Extracted molecule genomic DNA
Extraction protocol Chromatin associated with the target epitope was immunoprecipitated from mononucleosomal cell extract and amplified by TLAD.
Label Cy3
Label protocol The cDNA 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 input
Organism Saccharomyces cerevisiae
Characteristics strain: CYM36 (cdc7ts)
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 cDNA 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 ChIP and ChIP input 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 CYM36 cells bearing a cdc7 ts mutant were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia prewarmed to 37C containing 20ug/ml pronase (SIGMA).Cells were grown at 37C and harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated. Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody. As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition. The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 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 expression ratios were calculated to produce the values given in the data table.
 
Submission date Feb 12, 2010
Last update date Feb 26, 2010
Contact name Oliver Rando
E-mail(s) Oliver.Rando@umassmed.edu
Phone 508-856-8879
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 Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast

Data table header descriptions
ID_REF Probe ID
Block printing block
VALUE Block Normalized Log Ratio
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
2090542 3 -0.479546041 -0.633 100 3422 3595 1755 48 586 586 696 609 87 93 83 0 4819 4848 1734 35 421 421 466 277 59 99 98 0 0.645 0.680 0.683 0.612 2.583 0.701 0.528 342 742 91 7234 7436 2836 4398 3009 4427 1229403 1657999 4.760 15.819 0 0
2090544 11 -0.259658529 -0.977 95 2365 2469 1216 49 580 580 700 596 85 84 70 0 3952 4136 1462 35 438 438 478 270 56 99 99 0 0.508 0.511 0.525 0.467 2.542 0.500 0.418 295 653 25 5299 5587 1785 3514 1889 3698 728247 1220242 2.968 13.548 0 0
2090546 19 -0.154947237 -0.934 100 1622 1720 991 57 626 626 726 591 81 66 40 0 2311 2421 902 37 408 408 451 269 59 99 97 0 0.523 0.543 0.594 0.493 3.133 0.672 0.197 304 747 23 2899 3107 996 1903 1094 2013 523030 735880 1.682 7.323 0 0
2090548 27 0.112024924 -0.716 100 1428 1490 958 64 578 578 699 605 86 60 31 0 1807 1896 813 42 411 411 443 266 60 95 89 0 0.609 0.614 0.718 0.641 3.580 1.034 0.116 283 747 0 2246 2397 850 1396 912 1485 421781 536688 1.307 5.462 0 0
2090550 35 -0.036999091 -0.953 95 1290 1456 1029 70 597 597 727 630 86 55 28 0 1728 1769 691 39 386 386 424 251 59 97 89 0 0.516 0.621 0.651 0.616 3.640 1.747 0.065 228 686 28 2035 2242 693 1342 859 1383 332065 403350 1.157 5.359 0 0
2090552 43 0.103707253 -0.488 115 1341 1456 957 65 527 527 660 580 87 59 37 0 1530 1612 654 40 388 388 421 252 59 91 88 0 0.713 0.759 0.785 0.766 3.289 2.228 0.076 243 1154 0 1956 2153 814 1142 929 1224 353926 391671 1.372 4.726 0 0
2090554 3 -0.340115069 -0.602 100 1978 2212 1350 61 604 604 732 608 83 79 55 0 2514 2577 978 37 429 429 470 263 55 98 95 0 0.659 0.749 0.712 0.676 2.872 1.013 0.265 303 768 0 3459 3756 1374 2085 1608 2148 670107 780751 2.434 8.011 0 0
2090556 11 0.809 90 1905 2069 977 47 572 572 708 637 89 82 56 0 1225 1225 515 42 464 464 506 293 57 75 60 0 1.752 1.967 1.704 2.627 4.268 9.676 0.016 41 662 0 2094 2258 1333 761 1497 761 84839 50212 2.137 2.454 -100 1
2090558 19 1.457 75 1860 1904 818 42 597 597 703 550 78 87 56 0 897 921 357 38 437 437 486 304 62 68 37 0 2.746 2.700 3.420 2.980 3.522 13.121 0.011 32 473 17 1723 1791 1263 460 1307 484 60941 29485 2.184 1.431 -100 1
2090560 27 1.835 90 1994 1963 548 27 599 599 712 593 83 95 60 0 843 885 484 54 452 452 487 317 65 56 21 0 3.568 3.150 2.938 3.360 2.283 255.623 0.000 23 817 33 1786 1797 1395 391 1364 433 45150 20360 2.110 1.256 -100 1
2090562 35 Error 50 2283 2257 538 23 790 790 838 622 74 100 57 0 440 717 571 79 463 463 506 299 59 42 28 0 -64.913 5.776 1.299 1.282 2.018 82.700 0.000 7 237 76 1470 1721 1493 -23 1467 254 15799 5017 2.281 0.706 -100 1
2090564 43 1.293 80 1670 1742 570 32 619 619 736 645 87 78 37 0 828 884 525 59 399 399 435 266 61 56 43 0 2.450 2.315 1.914 2.532 4.669 116.157 0.000 32 587 16 1480 1608 1051 429 1123 485 55748 28295 1.560 1.688 -100 1
2090566 1 0.82635969 0.519 100 1813 1780 899 50 556 556 671 580 86 73 54 0 1340 1336 556 41 463 463 489 264 53 89 71 0 1.433 1.402 1.401 1.378 3.449 4.126 0.055 146 796 13 2134 2097 1257 877 1224 873 259879 195111 1.912 3.208 0 0
2090568 9 0.989 105 2003 2023 913 45 544 544 669 582 86 80 64 0 1172 1262 634 50 437 437 475 283 59 81 64 0 1.985 1.793 1.969 2.073 5.133 4.538 0.064 125 927 0 2194 2304 1459 735 1479 825 252843 157803 2.326 2.781 -100 1
2090570 17 1.037 95 1927 1948 940 48 532 532 686 595 86 80 55 0 1121 1197 569 47 441 441 486 290 59 78 55 0 2.051 1.873 1.986 1.801 3.778 5.445 0.056 108 718 48 2075 2172 1395 680 1416 756 210402 129229 2.121 2.452 -100 1
2090572 25 1.27435874 0.778 100 1976 2093 1045 49 536 536 654 570 87 83 61 0 1262 1322 572 43 422 422 456 259 56 86 75 0 1.714 1.730 1.724 1.759 3.160 3.283 0.171 239 812 22 2280 2457 1440 840 1557 900 500248 315952 2.525 3.344 0 0
2090574 33 1.12379347 0.645 100 2738 2888 1401 48 535 535 659 565 85 91 79 0 1835 1908 828 43 426 426 466 284 60 96 87 0 1.564 1.588 1.607 1.531 2.787 2.147 0.375 296 774 5 3612 3835 2203 1409 2353 1482 854824 564704 3.945 5.077 0 0
2090576 41 1.202812402 0.774 115 2058 2142 1082 50 536 536 662 587 88 83 64 0 1318 1408 666 47 428 428 466 271 58 89 75 0 1.710 1.639 1.692 1.629 3.318 3.121 0.159 289 1057 4 2412 2586 1522 890 1606 980 618990 406833 2.521 3.476 0 0
2090578 1 0.769693837 0.463 100 3315 3318 1591 47 534 534 652 547 83 94 85 0 2445 2493 1006 40 428 428 470 258 54 96 94 0 1.379 1.348 1.287 1.253 2.617 1.686 0.446 329 750 31 4798 4849 2781 2017 2784 2065 1091700 820224 4.874 7.841 0 0
2090580 9 0.623376268 0.031 100 2306 2530 1519 60 542 542 658 569 86 86 71 0 2153 2284 2001 87 427 427 457 260 56 98 94 0 1.022 1.071 1.054 1.018 2.850 0.914 0.389 308 748 48 3490 3845 1764 1726 1988 1857 779208 703417 3.290 7.027 0 0

Total number of rows: 25344

Table truncated, full table size 5785 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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