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Sample GSM76932 Query DataSets for GSM76932
Status Public on Oct 07, 2005
Title H2A.Z Biological Replicate 2 vs input | array 11_155
Sample type genomic
 
Channel 1
Source name aRNA-amplifed MNase digested ChIP input DNA
Organism Saccharomyces cerevisiae
Characteristics Strain: BY4741 bar1-
Extracted molecule genomic DNA
Label Cy3-aadUTP
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 QIAquick PCR purification 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 H2A.Z ChIP, 10 ul Ab, IVT #655
Organism Saccharomyces cerevisiae
Characteristics Strain: BY4741 bar1-
Extracted molecule genomic DNA
Label Cy5-aadUTP
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 QIAquick PCR purification 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.
 
 
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 Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green). DNA from a ChIP with 10 ul rabbit anti-H2A.Z was amplified using TLAD, and labeled with Cy5 fluorescent dye (red). These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.
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 Oct 04, 2005
Last update date Oct 06, 2005
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 GPL2626
Series (1)
GSE3411 H2A.Z marks the 5' end of genes

Data table header descriptions
ID_REF
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
493550 4 2.552703196 1.067 105 9378 9916 4287 43 191 191 203 96 47 100 100 0 4730 4790 2110 44 344 344 352 99 28 99 98 0 2.095 2.187 2.209 2.308 1.484 2.172 0.961 427 2124 96 13573 14171 9187 4386 9725 4446 4234030 2045518 101.177 44.828 0 0
493552 12 2.804850967 1.063 115 7805 8144 2974 36 190 190 200 93 46 100 100 0 4069 4314 1615 37 423 423 431 116 26 100 100 0 2.089 2.044 2.082 2.082 1.316 2.037 0.940 441 2562 94 11261 11845 7615 3646 7954 3891 3591564 1902380 85.419 33.474 0 0
493554 20 2.974065101 0.857 95 10968 11752 5630 47 181 181 193 88 45 100 100 0 6388 6828 3457 50 434 434 446 121 27 97 96 0 1.812 1.810 1.828 1.979 1.699 1.785 0.933 291 1914 91 16741 17965 10787 5954 11571 6394 3419846 1987054 131.352 52.744 0 0
493556 28 2.877211246 0.999 100 56648 52687 13994 26 172 172 183 88 48 100 100 34 28666 29503 14564 49 407 407 417 113 27 97 96 0 1.999 1.805 1.908 2.165 2.325 1.659 0.889 392 2072 92 84735 81611 56476 28259 52515 29096 20653363 11565266 596.636 257.398 0 0
493558 36 2.760190826 1.017 105 39984 44810 15367 34 165 165 172 82 47 100 100 23 20012 23939 11485 47 333 333 342 97 28 99 98 0 2.023 1.891 1.965 2.114 1.848 1.782 0.956 400 2180 91 59498 68251 39819 19679 44645 23606 17924073 9575763 544.366 243.268 0 0
493560 44 2.634367128 1.057 100 22409 22152 5300 23 139 139 149 73 48 100 100 0 10967 10974 2781 25 260 260 270 92 34 100 100 0 2.080 2.055 2.068 2.072 1.264 2.055 0.965 345 2106 95 32977 32727 22270 10707 22013 10714 7642324 3785938 301.411 116.348 0 0
493562 4 2.047336633 1.126 110 5582 5925 2535 42 193 193 205 98 47 100 100 0 2808 2964 1289 43 339 339 348 100 28 97 96 0 2.183 2.184 2.184 2.302 1.428 2.156 0.947 422 2234 94 7858 8357 5389 2469 5732 2625 2500456 1251018 58.367 26.160 0 0
493564 12 2.124080009 0.621 110 1339 1389 611 43 196 196 206 94 45 99 98 0 1164 1200 422 35 421 421 432 115 26 95 92 0 1.538 1.531 1.510 1.560 1.714 1.546 0.784 385 2251 93 1886 1972 1143 743 1193 779 534749 461930 12.585 6.678 0 0
493566 20 1.982566476 0.255 100 752 769 285 37 184 184 196 90 45 97 93 0 911 921 286 31 435 435 450 121 26 90 81 0 1.193 1.204 1.174 1.204 1.902 1.103 0.590 304 2175 93 1044 1071 568 476 585 486 233774 280004 6.367 3.893 0 0
493568 28 1.931961802 -0.027 105 2600 2733 1142 41 172 172 184 87 47 100 100 0 2887 3088 1062 34 413 413 421 110 26 100 100 0 0.981 0.957 0.953 0.931 1.422 0.974 0.908 375 2097 89 4902 5236 2428 2474 2561 2675 1024891 1158112 29.299 24.245 0 0
493570 36 1.375073103 -0.343 110 2399 2513 858 34 159 159 167 78 46 100 100 0 3172 3383 1219 36 331 331 339 91 26 100 100 0 0.788 0.771 0.779 0.780 1.272 0.748 0.936 400 2312 91 5081 5406 2240 2841 2354 3052 1005236 1353300 30.077 33.451 0 0
493572 44 1.453357686 -0.163 100 2710 2738 815 29 139 139 149 74 49 100 100 0 3149 3280 1074 32 270 270 280 95 33 100 100 0 0.893 0.863 0.858 0.874 1.312 0.840 0.928 360 2065 97 5450 5609 2571 2879 2599 3010 985538 1180876 34.986 31.579 0 0
493574 2 1.484518945 -0.073 100 449 467 189 40 179 179 190 91 47 87 67 0 617 639 179 28 333 333 342 104 30 88 69 0 0.951 0.941 0.903 0.872 2.621 0.909 0.330 309 2159 33 554 594 270 284 288 306 144346 197558 3.044 2.856 0 0
493576 10 1.952393617 0.063 110 584 600 220 36 184 184 198 109 55 94 79 0 783 812 210 25 400 400 418 176 42 89 57 0 1.044 1.010 1.006 0.982 2.258 0.788 0.464 343 2498 0 783 828 400 383 416 412 205805 278443 3.688 2.239 0 0
493578 18 2.890327973 0.971 105 3147 3148 999 31 173 173 184 85 46 100 100 0 1939 1983 548 27 422 422 437 134 30 100 100 0 1.960 1.906 1.869 1.919 1.319 1.931 0.906 357 2306 89 4491 4536 2974 1517 2975 1561 1123981 707784 34.871 11.537 0 0
493580 26 2.946615005 1.053 105 8941 9100 3976 43 160 160 169 82 48 100 100 0 4610 4690 1982 42 377 377 388 108 27 100 100 0 2.074 2.073 2.097 2.103 1.191 2.069 0.974 381 2262 97 13014 13253 8781 4233 8940 4313 3467200 1786842 108.915 39.833 0 0
493582 34 3.230516099 1.353 95 1725 1864 781 41 146 146 155 76 49 100 100 0 946 1061 377 35 328 328 336 98 29 99 98 0 2.555 2.344 2.382 2.409 1.471 2.377 0.837 302 1868 96 2197 2451 1579 618 1718 733 562929 320278 22.487 7.398 0 0
493584 42 3.245902096 1.195 105 1090 1198 571 47 124 124 134 78 58 100 99 0 661 706 245 34 239 239 248 75 30 98 95 0 2.289 2.300 2.280 2.314 1.870 2.526 0.721 357 2207 97 1388 1541 966 422 1074 467 427750 251922 13.641 6.107 0 0
493586 2 3.083651493 1.753 100 3019 3456 1499 43 187 187 199 98 49 100 100 0 1181 1291 458 35 341 341 352 104 29 99 98 0 3.371 3.441 3.433 3.530 1.402 3.524 0.896 337 2075 95 3672 4219 2832 840 3269 950 1164725 434915 33.235 9.029 0 0
493588 10 1.650609116 0.355 105 1051 1097 397 36 181 181 193 91 47 100 99 0 1096 1167 443 37 416 416 427 117 27 98 92 0 1.279 1.220 1.315 1.345 2.064 1.141 0.620 342 2134 93 1550 1667 870 680 916 751 375095 398965 9.934 6.325 0 0

Total number of rows: 24960

Table truncated, full table size 5718 Kbytes.




Supplementary data files not provided
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