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Sample GSM76934 Query DataSets for GSM76934
Status Public on Oct 07, 2005
Title H2A.Z Biological Replicate 1 vs input | array 11_123
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 2.196609706 1.110 105 5557 6362 3050 47 99 99 106 50 47 100 100 0 2633 2700 1115 41 104 104 108 35 32 100 100 0 2.158 2.413 2.312 2.402 1.398 2.546 0.922 383 2234 92 7987 8859 5458 2529 6263 2596 2436593 1033988 125.120 74.057 0 0
493552 12 2.364813341 2.365 115 18499 21986 10751 48 112 112 118 55 46 100 100 0 3689 4552 2132 46 121 121 125 40 32 100 99 0 5.153 4.937 4.787 4.988 1.411 5.071 0.947 449 2553 96 21955 26305 18387 3568 21874 4431 9871528 2043722 397.600 110.675 0 0
493554 20 2.30001979 2.217 100 8334 9713 5509 56 111 111 117 55 47 100 100 0 1894 2141 1261 58 125 125 129 41 31 98 97 0 4.648 4.763 4.859 5.239 1.546 4.717 0.955 303 2128 94 9992 11618 8223 1769 9602 2016 2943115 648614 174.473 49.073 0 0
493556 28 2.122687661 2.027 50 7237 9662 7664 79 108 108 118 61 51 100 100 0 1840 2303 1811 78 91 91 96 44 45 97 94 0 4.076 4.319 4.287 4.827 1.724 4.273 0.978 157 419 37 8878 11766 7129 1749 9554 2212 1516988 361641 156.459 50.159 -100 1
493558 36 2.136637328 2.277 110 23201 27607 14811 53 107 107 114 54 47 100 100 0 4878 5743 2835 49 112 112 115 34 29 100 100 0 4.846 4.884 4.781 4.857 1.251 5.006 0.978 400 2523 93 27860 33131 23094 4766 27500 5631 11042946 2297273 509.130 165.529 0 0
493560 44 2.076826807 2.168 105 17333 19070 8717 45 102 102 109 50 45 100 100 0 3936 4243 1806 42 102 102 106 31 29 100 100 0 4.494 4.581 4.466 4.641 1.396 4.706 0.959 363 2231 96 21065 23109 17231 3834 18968 4141 6922324 1540090 379.220 133.452 0 0
493562 4 2.193787364 0.989 105 8092 8988 4339 48 100 100 106 50 47 100 100 0 4128 4549 2062 45 102 102 107 34 31 100 100 0 1.985 1.999 1.989 2.008 1.262 2.039 0.962 389 2124 90 12018 13335 7992 4026 8888 4447 3496255 1769574 177.640 130.647 0 0
493564 12 1.948040277 2.023 115 4050 4516 2368 52 113 113 120 54 45 100 100 0 1085 1236 592 47 116 116 121 36 29 100 100 0 4.063 3.931 3.897 3.900 1.354 4.043 0.946 434 2373 95 4906 5523 3937 969 4403 1120 1960083 536293 81.407 30.972 0 0
493566 20 1.712130631 1.497 105 822 904 419 46 108 108 115 53 46 99 99 0 374 392 151 38 121 121 125 36 28 97 94 0 2.822 2.937 2.966 3.041 1.793 3.160 0.767 334 2176 95 967 1067 714 253 796 271 301922 130984 14.887 7.417 0 0
493568 28 1.208385712 1.143 100 824 951 436 45 102 102 110 54 49 100 100 0 433 479 206 43 106 106 106 43 40 100 97 0 2.208 2.276 2.408 2.325 1.634 2.334 0.736 123 2317 54 1049 1222 722 327 849 373 116937 58961 15.574 8.674 -100 1
493570 36 0.842786355 0.881 105 1250 1325 487 36 106 106 112 52 46 100 100 0 735 786 300 38 114 114 117 36 30 100 100 0 1.842 1.814 1.862 1.856 1.404 1.822 0.887 375 2091 95 1765 1891 1144 621 1219 672 496993 294765 23.327 18.583 0 0
493572 44 0.826277264 1.278 100 1544 1625 578 35 101 101 107 50 46 100 100 0 700 734 243 33 105 105 109 36 33 100 99 0 2.425 2.423 2.464 2.454 1.410 2.506 0.885 354 2017 95 2038 2153 1443 595 1524 629 575180 259715 30.360 17.361 0 0
493574 2 0.924187843 -0.632 95 485 516 214 41 92 92 101 55 54 99 96 0 699 767 291 37 90 90 95 37 38 100 100 0 0.645 0.626 0.637 0.600 1.597 0.621 0.791 331 1870 94 1002 1101 393 609 424 677 170768 253770 7.545 18.162 0 0
493576 10 1.619198909 0.797 110 1334 1367 616 45 100 100 108 53 49 100 100 0 816 817 310 37 106 106 109 34 31 100 100 0 1.738 1.782 1.775 1.723 1.412 1.872 0.901 427 2432 93 1944 1978 1234 710 1267 711 583891 348768 23.755 20.824 0 0
493578 18 2.614958614 2.107 100 3274 3044 1218 40 111 111 117 55 47 100 100 0 859 849 315 37 125 125 131 41 31 100 99 0 4.309 4.051 4.080 4.094 1.345 4.152 0.914 359 2155 92 3897 3657 3163 734 2933 724 1092684 304877 53.218 17.512 0 0
493580 26 2.607741694 2.562 100 5530 5241 2497 47 104 104 111 53 47 100 100 0 1035 1065 481 45 116 116 121 37 30 99 99 0 5.904 5.413 5.444 5.470 1.325 5.472 0.947 358 2137 91 6345 6086 5426 919 5137 949 1876156 381328 96.792 25.514 0 0
493582 34 2.876150811 2.560 90 8985 9266 4544 49 105 105 114 62 54 100 100 0 1618 1706 863 50 112 112 118 51 43 99 98 0 5.896 5.747 5.716 6.091 1.386 5.700 0.962 253 1863 96 10386 10755 8880 1506 9161 1594 2344306 431538 147.613 31.137 0 0
493584 42 2.576257178 2.515 105 9708 10024 4080 40 107 107 113 75 66 100 100 0 1789 1885 763 40 109 109 113 42 37 100 100 0 5.715 5.584 5.568 5.696 1.348 5.650 0.954 360 2237 91 11281 11693 9601 1680 9917 1776 3608747 678633 132.147 42.190 0 0
493586 2 2.798886598 0.554 100 3076 3352 1379 41 95 95 102 50 49 100 100 0 2121 2356 981 41 91 91 97 59 60 100 100 0 1.468 1.438 1.431 1.448 1.246 1.434 0.961 339 2065 91 5011 5522 2981 2030 3257 2265 1136183 798654 65.000 38.288 0 0
493588 10 1.888986852 0.975 105 2828 2854 1433 50 101 101 108 51 47 100 100 0 1492 1539 742 48 105 105 110 34 30 100 100 0 1.966 1.920 1.922 1.904 1.360 1.960 0.925 395 2006 97 4114 4187 2727 1387 2753 1434 1127465 607993 53.843 42.029 0 0

Total number of rows: 24960

Table truncated, full table size 5661 Kbytes.




Supplementary data files not provided
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