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Sample GSM509225 Query DataSets for GSM509225
Status Public on Feb 26, 2010
Title Series 1: H3k4me3 IP from alpha factor arrested 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 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 -0.072351291 0.011 55 4664 4687 2225 47 42 42 50 28 56 100 100 0 4641 4797 2131 44 54 54 56 20 35 99 99 0 1.008 0.979 0.948 0.939 1.970 0.991 0.920 101 129 95 9209 9388 4622 4587 4645 4743 473424 484532 165.607 237.050 0 0
2 1 -0.427579395 -0.344 50 166 199 136 68 47 47 50 19 38 93 81 0 205 244 141 57 54 54 58 22 37 97 90 0 0.788 0.800 0.769 0.723 3.322 0.825 0.363 88 60 58 270 342 119 151 152 190 17498 21450 7.842 8.455 0 0
3 1 -0.694280118 -0.610 55 114 151 114 75 38 38 45 19 42 83 74 0 171 229 161 70 55 55 57 19 33 96 90 0 0.655 0.649 0.632 0.655 3.272 0.557 0.428 104 86 70 192 287 76 116 113 174 15701 23783 5.579 9.053 0 0
4 1 -0.342272083 -0.258 55 183 217 133 61 40 40 49 28 57 96 84 0 225 279 188 67 54 54 56 19 33 98 93 0 0.836 0.787 0.750 0.821 2.991 0.635 0.428 100 66 36 314 402 143 171 177 225 21673 27889 6.000 11.737 0 0
5 1 -0.551779378 -0.467 60 159 199 157 78 44 44 48 18 37 89 78 0 209 247 155 62 50 50 54 19 35 92 89 0 0.723 0.787 0.738 0.644 4.212 0.855 0.390 100 114 55 274 352 115 159 155 197 19930 24683 8.389 10.158 0 0
6 1 -0.766542862 -0.683 55 161 238 235 98 42 42 47 18 38 90 84 0 243 308 249 80 52 52 56 29 51 95 88 0 0.623 0.766 0.619 0.635 4.842 0.715 0.163 92 111 50 310 452 119 191 196 256 21918 28371 10.611 8.690 0 0
7 1 -0.705335307 -0.621 55 149 198 160 80 43 43 45 16 35 87 82 0 213 254 161 63 50 50 53 18 33 97 95 0 0.650 0.760 0.772 0.631 3.666 0.821 0.422 94 66 48 269 359 106 163 155 204 18625 23914 9.563 11.167 0 0
8 1 -0.709781212 -0.627 50 165 202 145 71 40 40 47 27 57 88 83 0 245 282 154 54 52 52 56 18 32 97 96 0 0.648 0.704 0.692 0.638 2.710 0.718 0.437 85 59 46 318 392 125 193 162 230 17135 23999 5.741 12.556 0 0
9 1 -0.62336646 -0.540 55 153 184 127 69 45 45 49 21 42 88 79 0 205 253 167 66 48 48 50 15 30 98 96 0 0.688 0.678 0.629 0.623 2.999 0.602 0.366 89 110 48 265 344 108 157 139 205 16418 22473 6.429 13.533 0 0
10 1 -0.775835616 -0.691 55 138 172 133 77 42 42 46 17 36 86 76 0 210 263 168 63 55 55 56 19 33 98 97 0 0.619 0.625 0.492 0.509 3.519 0.521 0.256 94 90 61 251 338 96 155 130 208 16150 24741 7.412 10.895 0 0
11 1 -0.468430633 -0.385 60 152 184 123 66 41 41 44 18 40 91 84 0 203 258 171 66 58 58 60 19 31 93 86 0 0.766 0.715 0.667 0.689 3.831 0.532 0.271 91 117 41 256 343 111 145 143 200 16710 23504 7.778 10.421 0 0
12 1 1.450712754 1.535 55 4640 4284 1714 40 48 48 53 22 41 100 100 0 1636 1628 550 33 51 51 55 19 34 100 100 0 2.897 2.686 2.793 2.576 1.640 2.865 0.904 107 86 94 6177 5813 4592 1585 4236 1577 458340 174197 192.318 82.789 0 0
13 1 1.609472749 1.693 55 7351 6500 3032 46 48 48 49 16 32 100 100 0 2308 2292 744 32 50 50 54 18 33 100 100 0 3.234 2.878 3.080 2.436 2.361 3.290 0.859 102 109 89 9561 8694 7303 2258 6452 2242 662965 233746 403.188 124.333 0 0
14 1 1.5512109 1.635 55 20627 18993 7585 39 50 50 56 28 50 100 100 0 6681 6131 2502 40 56 56 59 27 45 100 99 0 3.106 3.118 3.087 3.232 1.667 3.141 0.964 105 87 93 27202 25018 20577 6625 18943 6075 1994285 643719 676.321 224.889 0 0
15 1 -0.563801906 -0.480 55 16243 15616 6617 42 41 41 53 47 88 100 100 0 22653 21552 9296 43 63 63 72 59 81 100 100 0 0.717 0.725 0.724 0.758 1.788 0.714 0.950 108 69 91 38792 37064 16202 22590 15575 21489 1686545 2327565 331.128 364.068 0 0
16 1 1.046425024 1.130 55 13840 13263 5106 38 47 47 69 109 157 100 100 0 6361 5807 2463 42 59 59 82 124 151 100 100 0 2.189 2.299 2.239 2.387 1.534 2.281 0.958 109 92 95 20095 18964 13793 6302 13216 5748 1445677 632988 121.046 46.169 0 0
17 1 1.603213758 1.687 55 15785 14692 6513 44 44 44 53 21 39 100 100 0 4944 4753 2043 42 56 56 62 33 53 99 99 0 3.220 3.119 3.264 3.379 3.094 3.353 0.851 105 92 86 20629 19345 15741 4888 14648 4697 1542624 499018 697.095 142.152 0 0
18 1 -0.661613929 -0.577 60 2374 2457 1203 48 51 51 56 24 42 99 98 0 3519 3672 1662 45 54 54 58 22 37 100 100 0 0.670 0.665 0.704 0.591 2.030 0.667 0.910 108 133 93 5788 6024 2323 3465 2406 3618 265325 396557 100.042 164.273 0 0
19 1 -0.674591783 -0.592 55 12890 15347 9378 61 57 57 124 205 165 99 99 0 19402 23387 13606 58 63 63 117 168 143 100 100 1 0.664 0.656 0.680 0.598 1.866 0.644 0.874 111 80 84 32172 38614 12833 19339 15290 23324 1703516 2595999 74.259 138.512 0 0
20 1 0.877 65 3682 4476 4518 100 52 52 137 749 546 68 65 0 2036 2875 3052 106 60 60 130 467 359 72 68 0 1.837 1.572 1.701 1.411 2.019 1.510 0.947 120 149 100 5606 7239 3630 1976 4424 2815 537074 344957 5.793 5.878 -100 1

Total number of rows: 45220

Table truncated, full table size 10185 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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