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Sample GSM509235 Query DataSets for GSM509235
Status Public on Feb 26, 2010
Title Series 4: H3k4me3 IP from alpha factor arrested wt cells 75min after switch to dextrose
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 -0.255137442 0.353 55 1342 1238 476 38 33 33 34 7 20 100 100 0 1061 1009 351 34 36 36 38 10 26 100 97 0 1.277 1.238 1.268 1.223 2.514 1.277 0.879 93 162 86 2334 2178 1309 1025 1205 973 115171 93848 172.000 97.100 0 0
2 1 -0.231 45 55 57 17 29 32 32 34 7 20 84 71 0 63 67 24 35 36 36 35 8 22 86 73 0 0.852 0.806 0.798 0.819 3.222 0.478 0.125 45 83 75 50 56 23 27 25 31 2561 3029 3.286 4.000 -100 1
3 1 0.064 45 54 60 28 46 31 31 32 6 18 84 71 0 57 63 27 42 35 35 36 8 22 85 69 0 1.045 1.036 1.022 0.846 3.734 0.962 0.122 63 71 38 45 57 23 22 29 28 3750 3960 4.667 3.375 -100 1
4 1 -0.177 45 55 58 22 37 32 32 33 7 21 79 65 0 62 62 16 25 36 36 36 9 25 81 65 0 0.885 1.000 0.999 1.022 2.743 1.077 0.147 44 73 69 49 52 23 26 26 26 2530 2740 3.571 2.889 -100 1
5 1 -1.369 45 46 53 23 43 34 34 34 7 20 60 41 0 68 75 31 41 37 37 37 9 24 93 75 0 0.387 0.500 0.450 0.507 3.170 0.266 0.075 48 78 71 43 57 12 31 19 38 2535 3605 2.714 4.222 -100 1
6 1 -1.126 50 43 51 26 50 32 32 34 7 20 61 42 0 61 65 21 32 37 37 36 9 25 84 66 0 0.458 0.679 0.645 0.608 3.440 0.749 0.157 63 95 59 35 47 11 24 19 28 3204 4092 2.429 3.222 -100 1
7 1 -0.907 50 50 53 17 32 34 34 34 7 20 71 52 0 67 78 36 46 37 37 37 8 21 91 76 0 0.533 0.463 0.511 0.637 3.636 0.248 0.107 46 99 70 46 60 16 30 19 41 2455 3588 2.714 5.125 -100 1
8 1 -0.848 50 47 54 28 51 32 32 33 9 27 60 46 0 65 72 27 37 38 38 38 10 26 80 65 0 0.556 0.647 0.779 0.685 3.960 0.624 0.171 41 126 79 42 56 15 27 22 34 2196 2958 2.333 3.400 -100 1
9 1 -0.807 50 54 59 21 35 34 34 34 6 17 85 82 0 73 78 24 30 38 38 36 9 25 96 82 0 0.571 0.625 0.645 0.578 3.131 0.413 0.137 28 137 84 55 65 20 35 25 40 1645 2171 4.167 4.667 -100 1
10 1 -0.678 50 49 57 28 49 34 34 34 9 26 58 41 0 62 62 18 29 38 38 39 9 23 75 60 0 0.625 0.958 0.765 0.719 6.168 1.310 0.107 41 114 51 39 47 15 24 23 24 2333 2541 2.556 2.556 -100 1
11 1 1.204 65 112 789 2440 309 36 36 39 12 30 91 79 0 70 153 362 236 37 37 37 10 27 81 66 0 2.303 6.491 2.750 2.217 6.661 2.287 0.927 48 212 16 109 869 76 33 753 116 37884 7363 62.500 11.600 -100 1
12 1 0.859383513 1.467 50 2162 2197 814 37 33 33 34 7 20 100 100 0 805 816 291 35 35 35 36 9 25 100 100 0 2.765 2.771 2.805 2.783 1.620 2.927 0.872 92 56 90 2899 2945 2129 770 2164 781 202157 75057 309.000 86.667 0 0
13 1 1.575431739 2.183 55 1560 1536 571 37 34 34 35 8 22 100 100 0 373 374 121 32 37 37 37 9 24 100 98 0 4.542 4.457 4.611 4.501 1.725 4.774 0.884 93 94 84 1862 1839 1526 336 1502 337 142856 34768 187.625 37.444 0 0
14 1 1.232466551 1.840 55 1717 1767 654 37 34 34 35 8 22 100 100 0 507 515 196 38 37 37 37 9 24 100 100 0 3.581 3.626 3.583 3.721 1.456 3.673 0.931 93 92 88 2153 2211 1683 470 1733 478 164287 47857 216.500 53.111 0 0
15 1 -1.518397817 -0.910 55 1263 1309 473 36 34 34 34 8 23 100 100 0 2349 2302 968 42 40 40 39 9 23 98 98 0 0.532 0.564 0.539 0.612 2.176 0.528 0.878 98 111 97 3538 3537 1229 2309 1275 2262 128329 225589 159.375 251.444 0 0
16 1 0.55946196 1.167 55 3117 3108 1121 36 33 33 34 8 23 100 100 0 1411 1396 560 40 38 38 38 8 21 99 99 0 2.246 2.264 2.249 2.487 1.992 2.263 0.923 101 85 84 4457 4433 3084 1373 3075 1358 313905 141027 384.250 169.750 0 0
17 1 1.56810759 2.176 50 2716 2739 1182 43 32 32 33 9 27 100 100 0 633 633 260 41 39 39 37 10 27 97 97 0 4.519 4.557 5.033 4.587 2.605 5.328 0.707 94 56 94 3278 3301 2684 594 2707 594 257425 59477 300.667 59.600 0 0
18 1 -0.947971409 -0.341 55 1720 1725 668 38 35 35 35 8 22 100 100 0 2171 2211 839 37 37 37 38 8 21 100 100 0 0.790 0.777 0.782 0.768 1.601 0.773 0.935 92 113 96 3819 3864 1685 2134 1690 2174 158695 203434 211.250 271.625 0 0
19 1 -1.179217557 -0.572 55 4802 4647 1898 40 34 34 35 7 20 100 100 0 7126 6918 3124 45 39 39 39 10 25 100 100 0 0.673 0.671 0.656 0.730 2.148 0.643 0.922 97 106 89 11855 11492 4768 7087 4613 6879 450721 671023 658.857 687.900 0 0
20 1 0.596870783 1.205 55 2239 2226 862 38 35 35 34 7 20 100 100 0 994 948 439 46 38 38 39 10 25 97 97 0 2.305 2.408 2.315 2.834 2.216 2.393 0.887 99 105 96 3160 3101 2204 956 2191 910 220413 93817 313.143 90.900 0 0

Total number of rows: 45220

Table truncated, full table size 9799 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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