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Sample GSM509228 Query DataSets for GSM509228
Status Public on Feb 26, 2010
Title Series 2: H3k4me3 IP from jhd2 delete cells 60min after release from arrest
Sample type other
 
Channel 1
Source name H3K4me3 IP
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741 bar1del jhd2del
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 jhd2del
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 and jhd2 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 YPD media 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 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) [email protected]
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 -0.772490818 -0.372 60 5707 5969 2898 48 45 45 54 35 64 100 100 0 7386 8004 3906 48 57 57 60 21 35 100 100 0 0.773 0.745 0.726 0.769 1.459 0.736 0.957 103 155 85 12991 13871 5662 7329 5924 7947 614821 824428 169.000 378.286 0 0
2 1 0.956 50 116 159 136 85 52 52 62 38 61 65 47 0 91 119 75 63 58 58 64 28 43 52 32 0 1.939 1.754 1.914 1.724 7.021 4.608 0.055 46 128 43 97 168 64 33 107 61 7325 5453 2.553 1.964 -100 1
3 1 -0.247 45 107 123 57 46 48 48 55 31 56 75 40 0 134 175 105 60 64 64 73 41 56 80 45 0 0.843 0.676 0.916 0.613 3.251 0.244 0.042 20 109 60 129 186 59 70 75 111 2465 3490 2.194 2.488 -100 1
4 1 0.147 45 100 116 70 60 38 38 51 29 56 73 51 0 113 137 83 60 57 57 60 24 40 83 63 0 1.107 0.975 1.176 0.940 4.855 0.744 0.123 49 70 64 118 158 62 56 78 80 5668 6690 2.241 3.208 -100 1
5 1 0.234 60 142 359 1317 366 42 42 51 25 49 81 73 0 141 208 250 120 56 56 64 56 87 68 40 0 1.176 2.086 1.445 1.176 3.991 5.573 0.660 72 125 49 185 469 100 85 317 152 25838 14960 12.320 2.571 -100 1
6 1 -0.193 55 88 110 62 56 46 46 51 23 45 72 47 0 102 124 81 65 54 54 60 24 40 76 47 0 0.875 0.914 0.951 0.970 3.592 0.716 0.190 59 142 56 90 134 42 48 64 70 6480 7312 2.565 2.667 -100 1
7 1 0.061 50 118 165 160 96 45 45 52 27 51 82 55 0 127 168 135 80 57 57 65 29 44 88 61 0 1.043 1.081 0.862 0.965 3.413 1.248 0.182 34 106 44 143 231 73 70 120 111 5610 5699 4.185 3.552 -100 1
8 1 2.780 35 153 161 49 30 50 50 64 50 78 87 50 0 95 118 81 68 80 80 82 33 40 25 12 0 6.867 2.921 5.084 3.231 3.665 5.475 0.007 8 84 74 118 149 103 15 111 38 1284 940 1.940 1.091 -100 1
9 1 -0.439 55 85 105 113 107 40 40 46 23 50 59 46 0 117 141 98 69 56 56 59 18 30 82 66 0 0.738 0.765 0.802 0.640 5.776 1.188 0.039 62 128 51 106 150 45 61 65 85 6514 8759 2.565 4.556 -100 1
10 1 -0.731 55 98 141 215 152 48 48 56 31 55 63 33 0 139 191 166 86 56 56 59 21 35 90 81 0 0.602 0.689 0.745 0.583 4.426 1.159 0.480 33 145 46 133 228 50 83 93 135 4645 6304 2.742 6.286 -100 1
11 1 -0.118 50 200 254 165 64 48 48 56 28 50 88 86 0 224 279 181 64 59 59 62 26 41 91 86 0 0.921 0.936 0.930 1.064 3.584 1.967 0.153 59 93 28 317 426 152 165 206 220 14961 16434 7.071 8.346 -100 1
12 1 1.335357264 1.736 55 6126 5926 2362 39 55 55 83 134 161 100 100 0 1883 1896 858 45 61 61 73 66 90 98 97 0 3.332 3.199 3.052 3.546 2.084 3.338 0.831 112 69 97 7893 7706 6071 1822 5871 1835 663751 212396 43.604 27.621 0 0
13 1 1.513150658 1.914 55 6805 6516 2665 40 48 48 58 30 51 100 100 0 1852 1847 982 53 59 59 63 24 38 93 91 0 3.769 3.617 3.315 4.947 3.546 3.790 0.752 103 97 95 8550 8256 6757 1793 6468 1788 671103 190256 215.267 74.333 0 0
14 1 1.372965188 1.774 50 16323 15402 5885 38 47 47 59 35 59 100 100 0 4815 4762 1688 35 56 56 59 19 32 100 100 0 3.420 3.263 3.244 3.274 1.712 3.417 0.934 100 41 93 21035 20061 16276 4759 15355 4706 1540178 476217 438.371 247.526 0 0
15 1 -1.330641809 -0.929 55 15898 15141 6241 41 64 64 68 39 57 100 100 0 30209 28265 10695 37 60 60 64 20 31 100 100 0 0.525 0.535 0.524 0.515 1.876 0.529 0.911 110 83 94 45983 43282 15834 30149 15077 28205 1665524 3109109 386.487 1410.050 0 0
16 1 0.095686851 0.496 55 16886 15257 6009 39 50 50 58 31 53 100 100 0 11989 10988 3419 31 55 55 59 20 33 100 100 0 1.411 1.391 1.419 1.219 2.008 1.461 0.931 106 105 92 28770 26140 16836 11934 15207 10933 1617257 1164772 490.290 546.450 0 0
17 1 1.139988016 1.541 55 15845 15144 4652 30 47 47 57 44 77 100 100 0 5485 5016 1810 36 57 57 62 25 40 100 100 0 2.910 3.044 2.958 3.259 1.590 3.051 0.926 111 103 95 21226 20056 15798 5428 15097 4959 1680954 556830 342.886 198.160 0 0
18 1 -0.530765067 -0.129 55 3587 3612 1427 39 48 48 52 25 48 100 100 0 3931 3943 2075 52 61 61 64 26 40 100 96 0 0.914 0.918 0.885 1.137 3.172 0.833 0.813 112 66 90 7409 7446 3539 3870 3564 3882 404551 441611 142.400 149.192 0 0
19 1 -1.02919352 -0.627 55 13022 12964 5170 39 48 48 55 33 60 100 100 0 20096 18563 8569 46 55 55 59 20 33 100 100 0 0.647 0.698 0.657 0.763 1.768 0.661 0.917 106 89 96 33015 31424 12974 20041 12916 18508 1374233 1967634 391.182 925.200 0 0
20 1 0.277942171 0.679 55 7711 7251 2953 40 55 55 63 39 61 100 99 0 4838 4478 1773 39 55 55 63 32 50 100 98 0 1.601 1.627 1.626 1.678 2.936 1.722 0.811 104 88 88 12439 11619 7656 4783 7196 4423 754120 465744 184.308 137.969 0 0

Total number of rows: 45220

Table truncated, full table size 10280 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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