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Sample GSM76933 Query DataSets for GSM76933
Status Public on Oct 07, 2005
Title H2A.Z Biological Replicate 2 vs input | array 11_156
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 2.358475862 0.138 110 1289 1333 470 35 212 212 227 116 51 98 97 0 1715 1709 534 31 736 736 748 167 22 93 90 0 1.100 1.152 1.138 1.131 1.711 1.065 0.665 396 2499 88 2056 2094 1077 979 1121 973 527671 676838 9.534 5.754 0 0
493552 12 2.532532085 0.289 110 1059 1140 430 37 210 210 222 111 50 99 97 0 1536 1582 407 25 841 841 848 191 22 93 84 0 1.222 1.255 1.252 1.283 1.853 1.129 0.599 410 2391 24 1544 1671 849 695 930 741 467260 648675 8.270 3.843 0 0
493554 20 2.805570338 0.215 95 6724 7214 3536 49 194 194 206 106 51 100 100 0 6259 6457 3012 46 635 635 644 157 24 100 99 0 1.161 1.206 1.190 1.251 1.463 1.198 0.938 279 1882 93 12154 12842 6530 5624 7020 5822 2012734 1801469 66.113 37.025 0 0
493556 28 2.815588699 0.625 105 40511 39667 10883 27 194 194 214 149 69 100 100 0 26713 26396 7246 27 574 574 590 288 48 100 100 0 1.542 1.529 1.534 1.528 1.212 1.528 0.977 382 2157 97 66456 65295 40317 26139 39473 25822 15152738 10083110 264.785 89.604 0 0
493558 36 2.707755331 0.606 105 41124 43649 16882 38 187 187 202 107 52 100 100 19 27398 31159 14339 46 504 504 513 136 26 99 99 0 1.522 1.418 1.440 1.460 1.180 1.367 0.971 402 2156 97 67831 74117 40937 26894 43462 30655 17547064 12525783 406.047 225.338 0 0
493560 44 2.553576826 0.462 105 20597 21180 8806 41 185 185 197 102 51 100 100 0 15279 16196 6344 39 462 462 472 125 26 100 100 0 1.378 1.334 1.289 1.323 1.205 1.345 0.971 357 2197 93 35229 36729 20412 14817 20995 15734 7561344 5781966 205.716 125.792 0 0
493562 4 1.987315694 -0.856 105 448 468 172 36 206 206 221 114 51 81 53 0 1171 1178 218 18 733 733 744 166 22 90 70 0 0.553 0.589 0.600 0.599 2.756 0.323 0.111 232 2039 1 680 707 242 438 262 445 108674 273346 2.167 2.614 -100 1
493564 12 2.075173593 -1.203 100 298 316 147 46 212 212 225 115 51 40 18 0 1035 1042 238 22 837 837 853 194 22 50 21 0 0.434 0.507 0.559 0.496 4.002 0.168 0.035 316 2085 100 284 309 86 198 104 205 99863 329289 0.791 0.974 -100 1
493566 20 2.052227263 -0.495 95 666 715 330 46 195 195 208 109 52 92 79 0 1293 1373 418 30 629 629 638 154 24 95 89 0 0.709 0.699 0.631 0.611 2.587 0.619 0.447 281 1822 83 1135 1264 471 664 520 744 200874 385738 4.651 4.773 0 0
493568 28 1.889686373 -0.637 110 1587 1612 479 29 194 194 207 105 50 99 99 0 2734 2756 639 23 568 568 581 148 25 100 100 0 0.643 0.648 0.656 0.636 1.444 0.635 0.845 387 2312 94 3559 3606 1393 2166 1418 2188 623998 1066411 13.381 14.696 0 0
493570 36 1.133024267 -1.021 110 1920 2006 602 30 183 183 198 106 53 100 100 0 4030 4157 1067 25 505 505 516 136 26 100 100 0 0.493 0.499 0.497 0.491 1.366 0.487 0.882 381 2265 93 5262 5475 1737 3525 1823 3652 764321 1583895 17.057 26.772 0 0
493572 44 1.190007783 -1.127 100 1624 1628 492 30 178 178 190 99 52 100 100 0 3620 3652 697 19 461 461 469 128 27 100 100 0 0.458 0.454 0.449 0.436 1.424 0.450 0.858 354 1997 93 4605 4641 1446 3159 1450 3191 576290 1292664 14.525 24.867 0 0
493574 2 1.486266085 -1.267 100 238 259 139 53 211 211 225 116 51 27 9 0 713 727 178 24 648 648 662 173 26 25 6 0 0.415 0.608 0.921 0.821 4.234 0.099 0.005 316 2304 100 92 127 27 65 48 79 81870 229658 0.293 0.376 -100 1
493576 10 1.872933785 -1.588 70 370 372 154 41 222 222 237 116 48 66 29 0 1185 1183 155 13 740 740 765 208 27 95 66 0 0.333 0.339 0.369 0.462 2.312 0.083 0.010 24 1174 45 593 593 148 445 150 443 8936 28384 1.164 2.010 -100 1
493578 18 2.72605089 -0.243 105 1074 1118 386 34 198 198 210 107 50 99 98 0 1690 1698 394 23 653 653 663 162 24 100 98 0 0.845 0.880 0.910 0.861 1.645 0.847 0.715 360 2340 97 1913 1965 876 1037 920 1045 402375 611320 8.486 6.389 0 0
493580 26 2.637050804 0.185 105 3025 3121 1411 45 183 183 194 103 53 100 100 0 3042 3150 1304 41 542 542 547 136 24 100 99 0 1.137 1.127 1.138 1.147 1.325 1.113 0.937 358 2234 95 5342 5546 2842 2500 2938 2608 1117222 1127821 28.417 19.140 0 0
493582 34 3.102430856 0.191 95 603 630 264 41 192 192 208 108 51 91 77 0 894 917 224 24 534 534 546 144 26 87 63 0 1.142 1.144 1.149 1.126 2.514 1.088 0.369 295 1836 93 771 821 411 360 438 383 185992 270629 3.907 2.576 0 0
493584 42 2.944104777 0.833 105 1343 1435 751 52 194 194 204 107 52 99 96 0 1157 1216 397 32 512 512 525 151 28 97 89 0 1.781 1.763 1.727 1.700 1.869 1.889 0.687 341 2187 97 1794 1945 1149 645 1241 704 489353 414757 11.505 4.576 0 0
493586 2 2.734538282 0.097 85 518 514 190 36 210 210 227 120 52 82 61 0 956 1010 282 27 668 668 676 167 24 79 45 0 1.069 0.889 1.188 0.950 3.644 0.456 0.041 86 1609 15 596 646 308 288 304 342 44228 86891 2.392 2.000 -100 1
493588 10 1.693579894 -1.067 100 488 523 226 43 204 204 219 110 50 82 63 0 1324 1395 398 28 729 729 741 181 24 94 77 0 0.477 0.479 0.493 0.457 3.071 0.322 0.257 303 2069 23 879 985 284 595 319 666 158518 422544 2.764 3.613 0 0

Total number of rows: 24960

Table truncated, full table size 5681 Kbytes.




Supplementary data files not provided

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