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Sample GSM509209 Query DataSets for GSM509209
Status Public on Feb 26, 2010
Title Series 3: H3k4me3 IP from cdc7ts cells 30min 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 -0.904962287 -0.450 95 6719 6944 3176 45 554 554 684 617 90 97 95 0 8855 9149 3193 34 434 434 467 268 57 100 100 0 0.732 0.733 0.720 0.654 2.160 0.747 0.707 329 643 96 14586 15105 6165 8421 6390 8715 2284643 3010122 10.146 32.396 0 0
2090544 11 -0.852088798 -0.630 90 3284 3477 1642 47 649 649 757 612 80 94 83 0 4589 4994 2224 44 511 511 553 286 51 99 99 0 0.646 0.631 0.642 0.612 2.334 0.598 0.533 293 533 31 6713 7311 2635 4078 2828 4483 1018907 1463221 4.444 15.528 0 0
2090546 19 -0.688652553 -0.581 100 4884 5249 2389 45 829 829 946 713 75 96 92 0 6711 7104 2941 41 645 645 686 344 50 100 100 0 0.668 0.684 0.688 0.658 1.890 0.676 0.652 349 739 94 10121 10879 4055 6066 4420 6459 1831815 2479311 6.035 18.657 0 0
2090548 27 -0.367300172 -0.332 100 6555 7166 3930 54 585 585 702 575 81 97 94 0 7961 9142 4542 49 444 444 483 272 56 100 100 0 0.794 0.757 0.755 0.701 1.942 0.763 0.782 325 764 48 13487 15279 5970 7517 6581 8698 2328959 2971237 11.242 31.835 0 0
2090550 35 -0.411510527 -0.257 90 8231 9125 4759 52 711 711 868 708 81 98 97 0 9507 10486 4666 44 518 518 544 287 52 100 100 0 0.837 0.844 0.840 0.793 1.774 0.872 0.786 291 569 96 16509 18382 7520 8989 8414 9968 2655251 3051442 11.662 34.641 0 0
2090552 43 -0.646161616 -0.437 95 5849 6305 2890 45 677 677 779 617 79 98 97 0 7421 8031 3271 40 417 417 451 264 58 99 99 0 0.738 0.739 0.730 0.714 1.945 0.744 0.731 307 665 93 12176 13242 5172 7004 5628 7614 1935686 2465663 8.956 28.712 0 0
2090554 3 -0.864210962 -0.405 95 2868 3061 1674 54 608 608 713 600 84 87 75 0 3424 3685 1343 36 432 432 450 250 55 100 100 0 0.755 0.754 0.742 0.659 2.645 0.863 0.466 304 660 34 5252 5706 2260 2992 2453 3253 930501 1120134 3.913 12.940 0 0
2090556 11 1.488 90 2117 2191 837 38 636 636 728 582 79 88 67 0 1058 1159 529 45 530 530 565 304 53 76 42 0 2.805 2.472 2.895 2.463 3.006 7.270 0.034 52 685 0 2009 2184 1481 528 1555 629 113909 60257 2.514 1.954 -100 1
2090558 19 1.092 70 2089 2325 959 41 927 927 1077 842 78 69 38 0 1191 1437 587 40 646 646 720 396 55 69 46 0 2.132 1.767 1.380 2.142 3.371 23.339 0.004 13 515 46 1707 2189 1162 545 1398 791 30227 18675 1.482 1.811 -100 1
2090560 27 0.922 80 1944 1941 904 46 648 648 778 637 81 76 51 0 1151 1180 444 37 467 467 523 331 63 83 55 0 1.895 1.813 1.706 1.673 2.525 6.773 0.031 43 563 0 1980 2006 1296 684 1293 713 83443 50744 1.826 1.985 -100 1
2090562 35 1.185 90 2439 2654 1542 58 823 823 917 705 76 81 56 0 1197 1457 840 57 486 486 550 336 61 86 59 0 2.273 1.886 2.368 1.936 3.905 6.908 0.040 72 656 0 2327 2802 1616 711 1831 971 191119 104929 2.464 2.699 -100 1
2090564 43 1.279 90 2008 2259 1129 49 627 627 742 645 86 83 55 0 972 1055 466 44 403 403 437 250 57 82 57 0 2.427 2.503 2.182 2.460 2.964 7.078 0.073 114 629 9 1950 2284 1381 569 1632 652 257563 120303 2.352 2.472 -100 1
2090566 1 0.731238026 1.094 100 3833 4019 1821 45 585 585 707 631 89 94 88 0 1975 2046 898 43 453 453 488 257 52 96 90 0 2.134 2.156 2.090 2.225 2.414 2.834 0.438 301 781 1 4770 5027 3248 1522 3434 1593 1209821 615949 5.249 6.062 0 0
2090568 9 0.994532244 1.262 110 2396 2556 1253 49 609 609 699 570 81 87 74 0 1173 1271 557 43 428 428 455 261 57 84 69 0 2.399 2.310 2.259 2.386 3.206 4.172 0.203 259 1011 0 2532 2790 1787 745 1947 843 661916 329120 3.258 3.126 0 0
2090570 17 0.865664349 1.034 90 2127 2231 1226 54 546 546 667 541 81 82 64 0 1185 1225 572 46 413 413 443 245 55 82 69 0 2.048 2.075 2.070 2.014 3.644 4.366 0.140 197 582 12 2353 2497 1581 772 1685 812 439433 241366 2.891 3.192 0 0
2090572 25 0.854096845 1.028 90 5398 5602 2411 43 572 572 694 606 87 98 96 0 2771 2854 1086 38 405 405 430 239 55 99 97 0 2.040 2.054 1.963 2.031 1.897 2.421 0.633 259 599 68 7192 7479 4826 2366 5030 2449 1450917 739185 8.099 10.142 0 0
2090574 33 1.514965579 1.755 95 13817 13785 4829 35 960 960 1074 793 73 99 99 0 4564 4648 1736 37 756 756 788 349 44 96 96 0 3.376 3.295 3.305 3.449 1.754 3.484 0.792 296 670 32 16665 16717 12857 3808 12825 3892 4080255 1375772 16.029 11.060 0 0
2090576 41 1.005238393 1.077 110 8442 8471 3244 38 646 646 756 617 81 99 98 0 4121 4107 1443 35 425 425 464 279 60 99 99 0 2.109 2.125 2.135 2.078 1.638 2.343 0.770 406 900 0 11492 11507 7796 3696 7825 3682 3439132 1667383 12.504 13.057 0 0
2090578 1 1.04726552 1.394 100 11702 11623 4556 39 517 517 669 587 87 99 98 0 4752 4634 1746 37 496 496 515 269 52 99 96 0 2.628 2.684 2.671 2.694 1.948 2.951 0.748 328 764 95 15441 15244 11185 4256 11106 4138 3812346 1519856 18.661 15.312 0 0
2090580 9 1.036994664 1.216 95 4565 4881 1996 40 496 496 630 561 89 98 96 0 2195 2286 842 36 443 443 479 273 56 97 94 0 2.322 2.379 2.252 2.417 2.120 2.873 0.564 288 673 41 5821 6228 4069 1752 4385 1843 1405707 658266 7.578 6.619 0 0

Total number of rows: 25344

Table truncated, full table size 5930 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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