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Sample GSM509226 Query DataSets for GSM509226
Status Public on Feb 26, 2010
Title Series 1: H3k4me3 IP from wt cells 60min after 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 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 -0.238185983 -0.338 55 5253 5074 1803 35 212 212 235 129 54 100 100 0 6608 6564 2062 31 234 234 286 158 55 100 100 0 0.791 0.768 0.762 0.749 1.492 0.777 0.920 88 142 84 11415 11192 5041 6374 4862 6330 446495 577591 37.512 39.734 0 0
2 1 -0.003 30 635 670 244 36 219 219 262 188 71 88 66 0 716 678 223 32 299 299 303 158 52 88 66 0 0.998 1.190 1.179 1.313 1.706 1.081 0.358 9 46 25 833 830 416 417 451 379 6029 6099 2.170 2.373 -100 1
3 1 -0.122 40 491 517 374 72 208 208 219 110 50 80 61 0 525 623 342 54 217 217 242 118 48 90 64 0 0.919 0.761 0.891 0.819 4.180 0.907 0.167 31 48 60 591 715 283 308 309 406 16021 19322 2.709 3.229 -100 1
4 1 -0.788 65 229 272 190 69 196 196 247 173 70 20 5 0 290 310 170 54 233 233 274 163 59 25 6 0 0.579 0.987 1.066 0.897 3.375 1.388 0.074 120 220 100 90 153 33 57 76 77 32606 37220 0.145 0.221 -100 1
5 1 0.400 25 242 278 169 60 180 180 226 157 69 33 16 0 337 380 183 48 290 290 289 139 48 33 16 0 1.319 1.089 0.885 0.572 4.254 1.160 0.112 12 28 100 109 188 62 47 98 90 3335 4556 0.331 0.655 -100 1
6 1 -0.314 65 233 267 144 53 159 159 195 138 70 32 15 0 302 334 166 49 210 210 237 149 62 34 13 0 0.804 0.871 0.764 0.880 4.165 0.591 0.045 120 180 100 166 232 74 92 108 124 32014 40041 0.522 0.651 -100 1
7 1 -0.631 35 525 619 322 52 237 237 270 166 61 66 50 0 720 744 232 31 274 274 304 149 49 100 83 0 0.646 0.813 0.657 0.601 2.809 1.029 0.159 6 99 77 734 852 288 446 382 470 3711 4466 2.102 2.953 -100 1
8 1 -0.095 30 471 405 156 38 222 222 247 115 46 71 57 0 563 656 188 28 297 297 308 115 37 100 57 0 0.936 0.510 1.153 1.070 1.431 0.547 0.131 7 55 46 515 542 249 266 183 359 2833 4592 1.374 3.026 -100 1
9 1 -0.178 30 500 511 111 21 172 172 202 113 55 100 85 0 573 555 107 19 202 202 237 141 59 100 85 0 0.884 0.960 1.000 0.963 1.807 0.847 0.230 7 34 79 699 692 328 371 339 353 3580 3885 2.735 2.255 -100 1
10 1 -0.555 65 203 219 130 59 171 171 215 150 69 15 5 0 260 277 130 46 213 213 242 171 70 17 1 0 0.681 0.750 0.999 0.900 3.638 0.708 0.049 120 167 100 79 112 32 47 48 64 26288 33198 0.027 0.205 -100 1
11 1 -0.267 65 237 274 220 80 178 178 235 174 74 20 6 0 282 331 230 69 211 211 248 145 58 31 11 0 0.831 0.800 1.200 1.232 3.382 1.280 0.133 120 159 100 130 216 59 71 96 120 32930 39674 0.224 0.572 -100 1
12 1 1.527134172 1.427 55 4279 4173 1201 28 160 160 205 187 91 100 100 0 1715 1687 536 31 183 183 220 136 61 97 96 0 2.689 2.668 2.760 2.817 1.799 2.798 0.830 98 80 88 5651 5517 4119 1532 4013 1504 408971 165296 21.219 10.787 0 0
13 1 2.204736548 2.105 50 5181 5011 1675 33 183 183 205 141 68 100 100 0 1349 1387 490 35 187 187 212 122 57 97 97 0 4.301 4.023 4.156 4.178 1.592 4.261 0.845 94 69 91 6160 6028 4998 1162 4828 1200 471050 130358 34.085 9.631 0 0
14 1 1.923813777 1.824 55 15125 13877 4685 33 152 152 187 134 71 100 100 0 4402 3936 1710 43 172 172 213 186 87 99 94 0 3.540 3.646 3.576 4.332 2.441 3.605 0.907 103 98 94 19203 17489 14973 4230 13725 3764 1429341 405395 102.164 20.016 0 0
15 1 -1.179219341 -1.278 55 15209 14792 5033 34 116 116 153 117 76 100 100 0 36794 34585 13185 38 187 187 212 128 60 100 100 0 0.412 0.427 0.412 0.443 1.962 0.402 0.910 103 86 86 51700 49074 15093 36607 14676 34398 1523579 3562219 125.120 268.539 0 0
16 1 0.941635054 0.842 50 14852 13504 4097 30 163 163 184 118 64 100 100 0 8379 7737 2459 31 182 182 197 94 47 100 100 0 1.792 1.766 1.730 1.789 1.674 1.794 0.911 98 54 88 22886 20896 14689 8197 13341 7555 1323348 758210 112.881 80.213 0 0
17 1 1.973090118 1.873 55 12646 11267 4232 37 154 154 183 148 80 100 100 0 3600 3476 871 25 190 190 233 145 62 100 100 0 3.663 3.382 3.720 3.098 1.974 3.910 0.814 99 105 96 15902 14399 12492 3410 11113 3286 1115480 344102 74.892 22.366 0 0
18 1 -0.591924269 -0.693 55 2184 2281 1069 46 160 160 206 145 70 95 93 0 3448 3972 1837 46 177 177 215 182 84 100 100 0 0.619 0.559 0.576 0.516 2.043 0.539 0.846 102 79 85 5295 5916 2024 3271 2121 3795 232660 405168 14.310 20.643 0 0
19 1 -0.693292359 -0.792 55 14660 13232 5210 39 154 154 193 142 73 100 98 0 25295 22467 7703 34 173 173 213 140 65 100 100 0 0.577 0.587 0.594 0.522 2.109 0.588 0.921 98 83 96 39628 35372 14506 25122 13078 22294 1296715 2201814 91.824 158.957 0 0
20 1 0.860498291 0.760 55 6738 6340 1730 27 150 150 188 142 75 100 100 0 4033 3691 1224 33 144 144 168 100 59 100 100 0 1.694 1.745 1.709 1.825 1.382 1.725 0.942 99 99 91 10477 9737 6588 3889 6190 3547 627694 365373 43.324 35.230 0 0

Total number of rows: 45220

Table truncated, full table size 10179 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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