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Sample GSM509213 Query DataSets for GSM509213
Status Public on Feb 26, 2010
Title Series 1: H3k4me3 IP from midlog wt cells
Sample type other
 
Channel 1
Source name H3K4me3 IP
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741 bar1del
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: BY4741 bar1del
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 BY4741 cells bearing a deletion in bar1 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 containing 20ug/ml pronase (SIGMA).Cells were 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 -0.930587629 -0.118 95 4023 4581 2339 51 933 933 1153 986 85 90 77 0 4605 4886 1845 37 1251 1251 1382 917 66 95 87 0 0.921 1.004 0.962 0.910 2.512 1.113 0.448 322 646 35 6444 7283 3090 3354 3648 3635 1475050 1573422 3.477 3.821 0 0
2090544 11 -0.537469394 0.149 95 5144 5395 2155 39 914 914 1036 763 73 98 93 0 5030 5203 1745 33 1215 1215 1274 835 65 97 92 0 1.109 1.124 1.122 1.114 1.927 1.165 0.566 291 656 40 8045 8469 4230 3815 4481 3988 1569955 1514136 5.713 4.705 0 0
2090546 19 -0.492331266 0.224 100 5249 5587 2619 46 952 952 1150 922 80 94 88 0 5080 5281 1720 32 1400 1400 1444 499 34 99 97 0 1.168 1.194 1.186 1.113 2.154 1.392 0.537 347 741 96 7977 8516 4297 3680 4635 3881 1938549 1832576 4.812 7.689 0 0
2090548 27 -0.475266652 0.380 105 5035 5234 2032 38 977 977 1119 778 69 97 93 0 4415 4578 1620 35 1297 1297 1375 535 38 97 94 0 1.301 1.297 1.286 1.282 1.971 1.409 0.543 315 881 12 7176 7538 4058 3118 4257 3281 1648796 1442102 5.289 5.987 0 0
2090550 35 -0.533706495 0.300 95 3588 3785 1629 43 938 938 1058 819 77 90 75 0 3326 3484 1342 38 1173 1173 1222 421 34 96 91 0 1.231 1.232 1.173 1.156 2.462 1.501 0.355 280 682 41 4803 5158 2650 2153 2847 2311 1059690 975412 3.330 5.373 0 0
2090552 43 -0.577838263 0.315 105 3984 4294 1922 44 942 942 1062 738 69 93 84 0 3457 3598 1211 33 1012 1012 1072 1250 116 87 49 0 1.244 1.296 1.265 1.218 2.377 1.219 0.308 311 870 55 5487 5938 3042 2445 3352 2586 1335531 1118865 4.379 2.021 0 0
2090554 3 -0.758747969 0.143 95 2762 2920 1517 51 980 980 1128 797 70 76 53 0 2891 2992 1011 33 1277 1277 1341 513 38 88 72 0 1.104 1.131 1.109 1.032 3.870 1.752 0.194 295 659 23 3396 3655 1782 1614 1940 1715 861327 882553 2.248 3.218 0 0
2090556 11 1.265 85 2130 2226 1019 45 907 907 996 696 69 78 44 0 1754 1906 579 30 1245 1245 1300 499 38 51 23 0 2.403 1.995 1.911 2.389 4.029 6.857 0.011 47 633 4 1732 1980 1223 509 1319 661 104626 89599 1.767 1.214 -100 1
2090558 19 -0.247 150 1045 1164 837 71 954 954 1099 828 75 19 4 0 1413 1481 540 36 1305 1305 1388 539 38 21 5 0 0.843 1.193 1.376 1.532 4.964 10.268 0.008 716 1700 100 199 386 91 108 210 176 833352 1060264 0.079 0.173 -100 1
2090560 27 2.890 60 3271 2952 872 29 981 981 1143 800 69 83 66 0 1685 1743 700 40 1376 1376 1481 1567 105 16 0 0 7.411 5.371 5.397 4.384 4.280 -0.011 0.000 6 373 73 2599 2338 2290 309 1971 367 17710 10459 2.261 0.167 -100 1
2090562 35 1.723 85 2626 2666 861 32 949 949 1057 779 73 90 66 0 1693 1728 512 29 1185 1185 1240 450 36 52 19 0 3.301 3.162 2.871 3.570 2.402 9.656 0.016 21 712 33 2185 2260 1677 508 1717 543 55985 36296 2.065 1.084 -100 1
2090564 43 1.674 110 2905 2979 1166 39 936 936 1086 758 69 93 72 0 1638 1639 515 31 1021 1021 1060 416 39 62 29 0 3.191 3.306 3.076 3.739 3.080 10.663 0.018 61 1168 0 2586 2661 1969 617 2043 618 181741 100006 2.497 1.392 -100 1
2090566 1 0.953 110 2470 2658 1361 51 861 861 969 695 71 80 62 0 1965 2061 756 36 1134 1134 1206 492 40 71 40 0 1.936 1.939 1.918 1.934 3.976 6.149 0.018 67 1108 0 2440 2724 1609 831 1797 927 178085 138097 2.430 1.738 -100 1
2090568 9 0.517 150 1080 1261 970 76 798 798 914 679 74 32 13 0 1361 1426 556 38 1164 1164 1228 494 40 28 9 0 1.431 1.767 1.732 1.576 5.018 10.770 0.007 716 1675 100 479 725 282 197 463 262 903024 1021258 0.511 0.401 -100 1
2090570 17 0.994 125 2359 2466 1148 46 795 795 944 719 76 79 57 0 1963 2043 649 31 1178 1178 1224 450 36 69 42 0 1.992 1.932 2.246 2.239 4.677 7.467 0.019 104 1456 0 2349 2536 1564 785 1671 865 256513 212425 2.117 1.820 -100 1
2090572 25 0.247021121 0.833 90 4017 4366 2061 47 730 730 832 639 76 93 91 0 2986 3017 860 28 1141 1141 1192 393 32 97 90 0 1.782 1.938 1.910 1.876 2.526 2.654 0.417 243 607 35 5132 5512 3287 1845 3636 1876 1060941 733198 5.531 4.644 0 0
2090574 33 0.554895339 1.306 100 7455 7755 3084 39 847 847 999 758 75 98 96 0 3910 3950 1454 36 1237 1237 1270 429 33 93 89 0 2.472 2.546 2.435 2.650 2.031 2.806 0.631 303 783 35 9281 9621 6608 2673 6908 2713 2349901 1196924 8.913 6.247 0 0
2090576 41 0.463013059 1.291 115 9812 10028 3918 39 764 764 886 677 76 99 97 0 4740 4774 1596 33 1042 1042 1068 408 38 96 95 0 2.447 2.482 2.501 2.501 2.085 2.778 0.699 407 1030 0 12746 12996 9048 3698 9264 3732 4081327 1942822 13.504 9.083 0 0
2090578 1 0.185427929 0.701 95 4243 4488 1975 44 851 851 929 680 73 95 90 0 3115 3299 1150 34 1028 1028 1098 488 44 97 89 0 1.625 1.601 1.612 1.503 2.404 1.967 0.457 292 664 25 5479 5908 3392 2087 3637 2271 1310377 963264 5.234 4.510 0 0
2090580 9 0.134517027 0.630 95 3684 3933 1694 43 749 749 862 688 79 96 86 0 3049 3119 1046 33 1153 1153 1219 499 40 94 83 0 1.548 1.620 1.592 1.600 2.266 2.001 0.400 293 666 43 4831 5150 2935 1896 3184 1966 1152305 913821 4.464 3.808 0 0

Total number of rows: 25344

Table truncated, full table size 5957 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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