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Sample GSM76930 Query DataSets for GSM76930
Status Public on Oct 07, 2005
Title H2A.Z Biological Replicate 1 vs input | array 11_130
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 #637
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 2.201452129 1.201 105 7625 8151 2834 34 65 65 68 24 35 100 100 0 3382 3597 1240 34 94 94 97 33 34 100 100 0 2.299 2.308 2.312 2.324 1.173 2.311 0.981 379 2218 93 10848 11589 7560 3288 8086 3503 3089396 1363340 336.792 106.061 0 0
493552 12 2.490438919 1.195 115 17432 18984 6840 36 64 64 69 28 40 100 100 0 7685 8276 2799 33 99 99 102 30 29 100 100 0 2.289 2.314 2.322 2.297 1.133 2.336 0.985 439 2592 93 24954 27097 17368 7586 18920 8177 8333923 3633089 675.536 272.467 0 0
493554 20 2.530407827 1.124 95 25622 25179 12248 48 64 64 69 27 39 100 100 0 11830 11224 5956 53 107 107 112 46 41 100 100 0 2.180 2.259 2.236 2.584 1.550 2.205 0.989 289 1925 93 37281 36232 25558 11723 25115 11117 7276740 3243656 930.000 241.565 0 0
493556 28 2.467209577 1.190 105 36282 39824 14739 37 66 66 72 32 44 100 100 7 15983 16882 6598 39 105 105 108 32 29 100 100 0 2.281 2.370 2.332 2.434 1.246 2.348 0.982 383 2217 95 52094 56535 36216 15878 39758 16777 15252649 6465806 1242.250 524.188 0 0
493558 36 2.463571597 1.313 105 36297 37419 12374 33 63 63 67 25 37 100 100 4 14678 14581 4997 34 94 94 97 26 26 100 100 0 2.485 2.579 2.553 2.653 1.345 2.576 0.976 383 2240 92 50818 51843 36234 14584 37356 14487 14331402 5584590 1494.080 557.077 0 0
493560 44 2.311345372 1.509 100 23746 25914 10769 41 60 60 63 21 33 100 100 0 8407 8986 3827 42 84 84 87 25 28 99 99 0 2.846 2.904 2.838 3.177 2.292 3.095 0.833 345 2146 97 32009 34756 23686 8323 25854 8902 8940311 3100203 1231.000 355.960 0 0
493562 4 1.996489364 0.668 105 8351 8892 3629 40 65 65 68 24 35 100 100 0 5310 5522 2297 41 94 94 97 28 28 100 100 0 1.589 1.626 1.629 1.640 1.199 1.619 0.976 388 2112 92 13502 14255 8286 5216 8827 5428 3450261 2142604 367.667 193.750 0 0
493564 12 2.121594762 0.601 115 2445 2479 932 37 66 66 70 26 37 100 100 0 1667 1770 690 38 98 98 102 31 30 100 100 0 1.516 1.443 1.436 1.462 1.192 1.430 0.968 413 2363 93 3948 4085 2379 1569 2413 1672 1023834 731076 92.654 53.806 0 0
493566 20 1.766545861 0.152 100 1506 1515 653 43 67 67 69 23 33 100 100 0 1408 1388 634 45 113 113 121 53 43 96 95 0 1.111 1.136 1.148 1.241 1.636 1.109 0.949 349 2038 94 2734 2723 1439 1295 1448 1275 528871 484250 62.870 23.906 0 0
493568 28 1.461266018 0.321 100 2156 2253 850 37 63 63 66 22 33 100 100 0 1778 1883 716 38 103 103 106 31 29 100 100 0 1.250 1.230 1.247 1.238 1.234 1.223 0.960 366 1959 93 3768 3970 2093 1675 2190 1780 824716 689291 99.409 57.323 0 0
493570 36 1.025805985 -0.005 105 1433 1438 463 32 61 61 64 21 32 100 100 0 1470 1488 467 31 93 93 96 27 28 100 100 0 0.996 0.987 0.998 0.986 1.312 0.984 0.936 371 2090 89 2749 2772 1372 1377 1377 1395 533582 551987 65.429 51.556 0 0
493572 44 1.057808927 0.323 100 1687 1689 501 29 59 59 62 20 32 100 100 0 1385 1357 444 32 84 84 87 25 28 99 99 0 1.251 1.280 1.314 1.347 1.964 1.279 0.847 346 2055 97 2929 2903 1628 1301 1630 1273 584247 469623 81.350 50.800 0 0
493574 2 1.18167109 -0.019 100 822 907 369 40 64 64 68 24 35 100 100 0 862 918 357 38 94 94 97 28 28 100 100 0 0.987 1.023 1.030 1.023 1.313 1.022 0.928 342 2144 94 1526 1667 758 768 843 824 310261 314115 34.958 29.321 0 0
493576 10 1.738313123 0.177 110 938 1004 409 40 63 63 66 23 34 100 100 0 875 946 377 39 101 101 105 31 29 100 100 0 1.130 1.114 1.106 1.123 1.278 1.106 0.939 421 2523 91 1649 1786 875 774 941 845 422673 398452 40.783 27.129 0 0
493578 18 2.695754545 0.991 100 4456 4518 1556 34 64 64 67 25 37 100 100 0 2315 2364 880 37 105 105 109 33 30 100 100 0 1.987 1.972 1.986 2.018 1.202 1.942 0.974 364 2199 95 6602 6713 4392 2210 4454 2259 1644683 860555 178.040 68.333 0 0
493580 26 2.71158096 1.207 100 11068 11203 3899 34 64 64 67 24 35 100 100 0 4868 4921 1722 34 103 103 107 34 31 100 100 0 2.309 2.312 2.283 2.352 1.279 2.311 0.974 366 2178 95 15769 15957 11004 4765 11139 4818 4100217 1801202 464.000 141.588 0 0
493582 34 2.920636539 1.523 85 13418 14065 5146 36 60 60 63 22 34 100 100 0 4739 4915 1819 37 92 92 96 28 29 100 100 0 2.875 2.904 2.872 2.963 1.234 2.907 0.975 243 1577 93 18005 18828 13358 4647 14005 4823 3417773 1194315 636.455 172.107 0 0
493584 42 2.811649845 1.766 110 16773 16939 7090 41 56 56 58 19 32 100 100 0 4993 4904 2060 42 79 79 82 36 43 99 99 0 3.402 3.499 3.468 3.760 2.145 3.698 0.870 365 2559 96 21631 21708 16717 4914 16883 4825 6182712 1789794 888.474 133.944 0 0
493586 2 2.661736068 1.631 100 8303 8531 2814 32 64 64 67 23 34 100 100 0 2756 2829 916 32 95 95 98 29 29 100 100 0 3.096 3.097 3.134 3.118 1.303 3.132 0.961 338 2051 90 10900 11201 8239 2661 8467 2734 2883332 956282 368.000 94.172 0 0
493588 10 1.672859259 -0.133 105 1450 1542 527 34 64 64 67 23 34 100 100 0 1619 1734 686 39 99 99 103 29 28 100 100 0 0.912 0.904 0.929 0.931 1.340 0.871 0.910 346 2084 95 2906 3113 1386 1520 1478 1635 533677 600017 64.130 56.241 0 0

Total number of rows: 24960

Table truncated, full table size 5700 Kbytes.




Supplementary data files not provided
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