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Sample GSM509227 Query DataSets for GSM509227
Status Public on Feb 26, 2010
Title Series 2: H3k4me3 IP from alpha factor arrested jhd2 delete cells
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) 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 -0.342537265 -0.433 50 4384 4424 1060 23 1277 1277 1332 479 35 100 100 0 5334 5235 1291 24 1140 1140 1202 407 33 100 97 0 0.741 0.768 0.680 0.777 1.655 0.765 0.745 90 79 85 7301 7242 3107 4194 3147 4095 398135 471173 6.455 9.909 0 0
2 1 0.15617873 0.067 55 2322 2377 544 22 1038 1038 1076 368 34 99 89 0 2213 2267 491 21 987 987 1047 326 31 98 93 0 1.047 1.046 1.033 1.079 1.945 1.071 0.626 104 79 87 2510 2619 1284 1226 1339 1280 247243 235771 3.535 3.742 0 0
3 1 0.203617787 0.113 55 2355 2386 593 24 1042 1042 1086 358 32 97 87 0 2170 2182 665 30 956 956 1023 296 28 91 88 0 1.082 1.096 0.918 1.116 2.694 1.133 0.358 102 80 90 2527 2570 1313 1214 1344 1226 243399 222567 3.631 3.916 0 0
4 1 0.245 50 2572 2581 527 20 1059 1059 1158 487 42 98 87 0 2318 2325 406 17 1041 1041 1123 410 36 98 89 0 1.185 1.185 1.177 1.170 1.597 1.208 0.597 78 81 47 2790 2806 1513 1277 1522 1284 201347 181333 2.922 2.932 -100 1
5 1 0.250837476 0.161 55 2343 2469 837 33 1063 1063 1090 335 30 94 84 0 2232 2389 1022 42 1087 1087 1107 322 29 96 87 0 1.118 1.080 1.139 1.113 1.836 0.963 0.342 96 80 74 2425 2708 1280 1145 1406 1302 237070 229330 4.116 3.981 0 0
6 1 0.277685034 0.188 55 2353 2335 498 21 1027 1027 1067 326 30 98 92 0 2150 2261 501 22 986 986 1069 378 35 100 91 0 1.139 1.026 0.962 1.016 1.578 1.041 0.666 89 116 90 2490 2583 1326 1164 1308 1275 207851 201223 3.890 3.153 0 0
7 1 0.141 50 2294 2339 400 17 1089 1089 1246 889 71 82 7 0 2140 2175 491 22 1047 1047 1227 1071 87 51 3 0 1.102 1.108 1.042 1.123 1.694 0.874 0.250 64 77 52 2298 2378 1205 1093 1250 1128 149681 139224 1.229 0.885 -100 1
8 1 -0.018 50 2280 2342 520 22 1067 1067 1078 417 38 96 87 0 2211 2205 452 20 983 983 1023 318 31 96 90 0 0.988 1.043 0.920 1.052 1.915 1.121 0.512 65 106 51 2441 2497 1213 1228 1275 1222 152255 143301 3.031 3.717 -100 1
9 1 0.122 55 2422 2680 1172 43 1093 1093 1128 418 37 96 90 0 2254 2569 1402 54 1033 1033 1096 346 31 98 85 0 1.088 1.033 1.063 1.153 2.057 0.962 0.544 60 123 65 2550 3123 1329 1221 1587 1536 160812 154115 3.713 4.257 -100 1
10 1 0.107 45 2376 3321 6891 207 950 950 1056 508 48 100 83 0 2229 3300 8257 250 905 905 994 382 38 96 88 1 1.077 0.990 1.045 1.160 2.325 0.718 0.010 59 59 51 2750 4766 1426 1324 2371 2395 195933 194722 4.459 6.037 -100 1
11 1 0.219 50 2481 2515 447 17 1074 1074 1135 403 35 100 89 0 2219 2294 451 19 1010 1010 1094 442 40 95 82 0 1.164 1.122 1.123 1.153 1.744 1.137 0.571 47 105 57 2616 2725 1407 1209 1441 1284 118203 107820 3.424 2.715 -100 1
12 1 0.860534934 0.771 50 3757 3861 779 20 1131 1131 1132 369 32 100 100 0 2544 2629 555 21 1005 1005 1042 354 33 98 96 0 1.706 1.681 1.639 1.724 1.489 1.739 0.749 89 57 88 4165 4354 2626 1539 2730 1624 343636 234017 7.396 4.483 0 0
13 1 1.235268673 1.145 50 5111 5071 1245 24 968 968 987 317 32 100 100 0 2749 2936 1392 47 876 876 929 330 35 100 97 0 2.212 1.992 2.072 2.132 1.421 1.757 0.700 93 72 89 6016 6163 4143 1873 4103 2060 471559 273003 12.883 6.082 0 0
14 1 1.514839376 1.425 55 10297 10020 2295 22 906 906 966 372 38 100 100 0 4412 4137 1264 30 914 914 930 323 34 95 92 0 2.685 2.828 2.668 3.035 2.067 2.888 0.771 91 116 94 12889 12337 9391 3498 9114 3223 911850 376426 24.339 9.929 0 0
15 1 -0.710960071 -0.800 55 9595 9250 2557 27 982 982 1028 337 32 97 96 0 15904 15295 4526 29 909 909 952 350 36 98 98 0 0.574 0.575 0.576 0.555 2.649 0.546 0.823 94 112 83 23608 22654 8613 14995 8268 14386 869534 1437708 24.398 40.980 0 0
16 1 0.333586368 0.243 55 7762 7432 1910 25 829 829 931 404 43 98 97 0 6713 6600 1810 27 856 856 898 351 39 100 97 0 1.184 1.150 1.155 1.123 2.289 1.143 0.799 92 94 94 12790 12347 6933 5857 6603 5744 683736 607244 16.092 16.245 0 0
17 1 0.850351162 0.761 55 10256 9478 3060 32 839 839 884 363 41 98 96 0 6371 6174 1388 22 813 813 828 291 35 100 100 0 1.694 1.611 1.644 1.531 1.619 1.719 0.894 93 91 96 14975 14000 9417 5558 8639 5361 881414 574212 23.675 18.371 0 0
18 1 0.075417718 -0.014 50 2761 2783 641 23 904 904 930 352 37 100 96 0 2688 2787 736 26 813 813 892 377 42 98 95 0 0.990 0.952 0.992 0.981 1.699 0.955 0.765 88 58 80 3732 3853 1857 1875 1879 1974 244918 245263 5.264 5.027 0 0
19 1 -0.368072357 -0.458 50 9568 9423 2639 28 774 774 772 262 33 100 100 0 12741 12367 3588 29 665 665 746 344 46 100 100 0 0.728 0.739 0.737 0.738 1.640 0.724 0.859 90 57 88 20870 20351 8794 12076 8649 11702 848113 1113032 33.019 33.782 0 0
20 1 0.723115974 0.633 55 6526 6489 1562 24 757 757 814 353 43 100 100 0 4495 4351 1451 33 776 776 813 323 39 98 96 0 1.551 1.603 1.551 1.718 1.599 1.544 0.856 95 113 96 9488 9307 5769 3719 5732 3575 616450 413319 16.076 10.954 0 0

Total number of rows: 45220

Table truncated, full table size 10142 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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