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Sample GSM509237 Query DataSets for GSM509237
Status Public on Feb 26, 2010
Title Series 4: H3k4me3 IP from wt cells 75min after switch to dextrose and release from arrest
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 YPgalactose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were filtered on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDextrose media containing 20ug/ml pronase (SIGMA) or 1ug/ml alfa factor. 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 4x44 agilent S.cerevisiae whole genome arrays.
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 GPL4131
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
1 1 -0.106963961 0.127 55 695 665 232 34 32 32 32 5 15 100 100 0 644 672 252 37 37 37 38 13 34 100 100 0 1.092 0.997 0.972 1.011 1.345 0.982 0.941 92 144 86 1270 1268 663 607 633 635 61139 61812 126.600 48.769 0 0
2 1 -0.392 40 47 50 15 30 31 31 32 8 25 69 46 0 59 61 13 21 38 38 38 12 31 76 46 0 0.762 0.826 0.762 0.685 4.349 0.284 0.048 13 87 49 37 42 16 21 19 23 647 789 2.250 1.917 -100 1
3 1 -1.000 40 43 42 10 23 31 31 31 6 19 70 35 0 62 61 14 22 38 38 39 11 28 76 58 0 0.500 0.478 0.532 0.570 3.409 0.187 0.060 34 54 56 36 34 12 24 11 23 1418 2073 1.833 2.000 -100 1
4 1 -1.222 65 34 34 8 23 31 31 32 7 21 30 10 0 44 45 15 33 37 37 38 11 28 35 15 0 0.429 0.375 0.364 0.466 3.373 -0.058 0.005 120 194 100 10 11 3 7 3 8 4136 5352 0.286 0.636 -100 1
5 1 -1.585 65 33 34 7 20 31 31 32 6 18 19 5 0 45 45 15 33 39 39 39 12 30 28 11 0 0.333 0.500 0.400 0.403 3.553 -0.031 0.002 120 240 100 8 9 2 6 3 6 4067 5423 0.333 0.500 -100 1
6 1 -2.644 60 36 37 6 16 32 32 33 7 21 30 8 0 62 60 11 18 37 37 38 13 34 80 36 0 0.160 0.217 0.265 0.247 2.891 0.061 0.007 36 207 47 29 28 4 25 5 23 1325 2156 0.571 1.692 -100 1
7 1 -1.059 35 43 43 9 20 31 31 33 7 21 60 39 0 57 55 12 21 32 32 33 10 30 85 56 0 0.480 0.522 0.528 0.560 3.078 0.156 0.027 41 23 41 37 35 12 25 12 23 1758 2238 1.429 2.200 -100 1
8 1 -2.000 65 34 35 10 28 32 32 33 7 21 28 7 0 46 46 14 30 38 38 38 11 28 42 9 0 0.250 0.375 0.600 0.527 3.219 0.100 0.009 120 231 100 10 11 2 8 3 8 4210 5548 0.286 0.727 -100 1
9 1 Error 65 33 34 9 26 33 33 34 8 23 14 3 0 41 43 15 34 40 40 40 13 32 22 9 0 0.000 0.333 0.500 0.629 2.786 0.091 0.009 120 205 100 1 4 0 1 1 3 4128 5114 0.000 0.231 -100 1
10 1 -0.064 25 54 56 8 14 32 32 34 6 17 100 100 0 59 62 10 16 36 36 39 10 25 100 62 0 0.957 0.923 1.128 0.926 1.607 0.195 0.035 8 20 0 45 50 22 23 24 26 445 495 3.667 2.300 -100 1
11 1 -0.263 65 37 41 20 48 32 32 34 8 23 36 15 0 45 46 13 28 39 39 39 13 33 27 8 0 0.833 1.286 0.778 0.824 4.015 46.623 0.765 120 166 100 11 16 5 6 9 7 4979 5494 0.875 0.538 -100 1
12 1 1.655147281 1.889 55 1131 1174 437 37 31 31 34 8 23 100 100 0 335 333 135 40 38 38 39 13 33 100 100 0 3.704 3.875 3.913 4.106 1.428 3.815 0.934 99 89 87 1397 1438 1100 297 1143 295 116232 33003 142.500 22.615 0 0
13 1 2.434863092 2.669 55 777 802 343 42 33 33 33 6 18 100 100 0 155 157 60 38 38 38 37 11 29 97 95 0 6.359 6.462 6.189 6.719 1.777 6.819 0.798 97 92 83 861 888 744 117 769 119 77755 15277 128.167 10.909 0 0
14 1 1.722491616 1.956 55 910 875 348 39 33 33 33 6 18 100 100 0 262 251 110 43 36 36 36 11 30 94 92 0 3.881 3.916 3.773 4.169 2.073 3.998 0.847 95 90 93 1103 1057 877 226 842 215 83133 23890 140.333 19.545 0 0
15 1 -1.719940838 -1.487 55 941 909 431 47 33 33 33 6 18 98 97 0 2582 2630 834 31 36 36 38 12 31 100 100 0 0.357 0.338 0.366 0.265 2.789 0.342 0.835 97 110 88 3454 3470 908 2546 876 2594 88152 255148 146.000 216.000 0 0
16 1 1.220765511 1.455 55 2167 2129 887 41 32 32 33 6 18 100 100 0 820 833 305 36 41 41 39 13 33 100 98 0 2.741 2.648 2.695 2.586 1.444 2.747 0.953 96 84 88 2914 2889 2135 779 2097 792 204350 79930 349.333 61.077 0 0
17 1 2.060904454 2.295 55 1977 1913 830 43 34 34 35 9 25 100 100 0 432 425 124 29 36 36 37 12 32 100 100 0 4.907 4.830 5.070 4.536 1.636 5.517 0.864 94 111 96 2339 2268 1943 396 1879 389 179807 39981 208.667 32.333 0 0
18 1 -0.992706782 -0.758 55 1464 1555 529 34 32 32 34 8 23 100 100 0 2461 2470 1127 45 39 39 39 13 33 100 100 0 0.591 0.626 0.585 0.684 1.639 0.576 0.904 99 109 96 3854 3954 1432 2422 1523 2431 153949 244490 190.125 187.000 0 0
19 1 -0.942333259 -0.709 55 3335 3337 1260 37 31 31 33 7 21 100 100 0 5439 5239 2521 48 37 37 39 12 30 100 100 0 0.612 0.636 0.610 0.718 1.752 0.592 0.939 97 104 91 8706 8508 3304 5402 3306 5202 323703 508208 472.000 433.333 0 0
20 1 1.007903366 1.242 55 1788 1749 533 30 33 33 34 7 20 100 100 0 779 733 277 37 37 37 39 12 30 100 98 0 2.365 2.466 2.423 2.651 1.502 2.419 0.947 94 108 93 2497 2412 1755 742 1716 696 164451 68942 245.000 57.833 0 0

Total number of rows: 45220

Table truncated, full table size 9811 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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