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Sample GSM363571 Query DataSets for GSM363571
Status Public on Jan 28, 2009
Title ChIP Input cell cycle CCA, 40 min | array na_13_079
Sample type genomic
 
Channel 1
Source Name Amplified sonicated DNA
Organism(s) Saccharomyces cerevisiae
Characteristics Strain: BY4741 bar1(del)
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 Cy3
Label protocol The DNA 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 40 min
Organism(s) Saccharomyces cerevisiae
Characteristics Strain: BY4741 bar1(del)
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 DNA 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, labeled ChIP DNA 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 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours. To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase. Upon release, cells were harvested after 40 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated. Extracts of these cells were then digested with MNase (ChIP Input). As a reference, DNA was obtained from sonication of unsynchronized cells. The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.
Data processing After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy5/Cy3) were calculated to produce the values given in the data table.
 
Submission date Jan 23, 2009
Contact name Oliver Rando
E-mail(s) Oliver.Rando@umassmed.edu
Phone 508-856-8879
Fax 1-508-856-6464
Organization name UMass Medical School
Street address 364 Plantation St.
City Worcester
State/province MA
ZIP/Postal code 01605-4321
Country USA
 
Platform ID GPL2625
Series (1)
GSE14565 Lack of epigenetic maintenance of active chromatin states in budding yeast

Data table header descriptions
ID_REF Probe ID
Block printing block
VALUE Block Normalized Log2 Ratio (635/532)
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 1.782018961 0.155 105 3324 3238 1132 34 297 297 315 164 52 99 99 0 2996 2810 1096 39 277 277 284 75 26 95 94 0 1.113 1.161 1.159 1.250 1.953 1.140 0.855 393 2195 92 5746 5474 3027 2719 2941 2533 1272488 1104491 17.823 33.680 0 0
493552 12 1.111803516 0.334 115 3406 3375 1195 35 303 303 328 177 53 99 99 0 2732 2697 1038 38 271 271 283 94 33 97 95 0 1.261 1.266 1.269 1.304 1.729 1.261 0.844 432 2562 96 5564 5498 3103 2461 3072 2426 1458204 1165091 17.215 25.681 0 0
493554 20 0.618407314 0.932 100 6046 5789 2559 44 296 296 316 167 52 100 99 0 3283 3076 1521 49 270 270 282 86 30 93 91 0 1.908 1.958 1.919 2.099 2.064 1.973 0.832 347 2066 96 8763 8299 5750 3013 5493 2806 2008708 1067343 32.772 32.488 0 0
493556 28 0.641915436 1.472 105 6458 6312 1984 31 279 279 299 165 55 100 100 0 2479 2404 926 38 252 252 264 93 35 96 96 0 2.775 2.803 2.789 3.090 1.858 2.812 0.860 422 2166 95 8406 8185 6179 2227 6033 2152 2663506 1014660 36.442 23.011 0 0
493558 36 -0.172640217 1.219 105 9800 9514 4197 44 262 262 279 150 53 100 100 0 4328 4284 2147 50 231 231 239 80 33 95 94 0 2.328 2.283 2.283 2.574 1.793 2.228 0.936 411 2219 91 13635 13305 9538 4097 9252 4053 3910128 1760800 61.567 50.563 0 0
493560 44 0.472979033 1.534 105 10035 10367 3506 33 255 255 275 158 57 100 100 0 3601 3779 1315 34 223 223 231 74 32 100 100 0 2.895 2.844 2.805 2.898 1.385 2.876 0.931 390 2178 92 13158 13668 9780 3378 10112 3556 4043155 1473715 63.873 47.946 0 0
493562 4 1.158262038 1.350 105 4063 4291 1671 38 301 301 323 166 51 100 99 0 1751 1848 844 45 275 275 283 77 27 95 95 0 2.549 2.537 2.509 2.697 1.730 2.518 0.842 388 2075 90 5238 5563 3762 1476 3990 1573 1664732 717205 23.904 20.325 0 0
493564 12 0.993263199 -0.227 105 1422 1538 708 46 309 309 328 171 52 97 93 0 1581 1850 805 43 278 278 292 93 31 99 98 0 0.854 0.782 0.786 0.754 2.062 0.784 0.682 370 1993 97 2416 2801 1113 1303 1229 1572 569129 684472 7.076 16.753 0 0
493566 20 0.651063366 -2.000 100 1036 1085 433 39 294 294 316 165 52 95 85 0 3229 3538 1553 43 260 260 270 81 30 100 99 0 0.250 0.241 0.231 0.236 2.271 0.211 0.610 320 1991 97 3711 4069 742 2969 791 3278 347336 1132044 4.661 40.346 0 0
493568 28 0.458183917 -2.185 105 953 977 373 38 269 269 292 160 54 95 85 0 3368 3475 1206 34 258 258 269 86 31 99 99 0 0.220 0.220 0.223 0.209 1.883 0.199 0.620 404 1999 92 3794 3925 684 3110 708 3217 394759 1404044 4.281 37.279 0 0
493570 36 0.815162961 -2.596 105 1248 1289 523 40 264 264 284 157 55 97 91 0 6183 6251 2643 42 235 235 243 78 32 99 98 0 0.165 0.170 0.168 0.173 1.882 0.159 0.772 345 2059 94 6932 7041 984 5948 1025 6016 444801 2156705 6.401 77.026 0 0
493572 44 -1.066459406 -2.239 105 1539 1615 529 32 254 254 278 159 57 99 99 0 6290 6424 1728 26 223 223 230 75 32 100 100 0 0.212 0.219 0.218 0.210 1.464 0.210 0.820 367 2091 95 7352 7562 1285 6067 1361 6201 592875 2357667 8.409 82.587 0 0
493574 2 -0.110906875 Error 100 267 325 227 69 253 253 283 174 61 24 8 0 122 373 603 161 147 147 207 195 94 24 13 0 -0.560 0.319 1.011 0.807 3.919 0.294 0.240 316 2312 100 -11 298 14 -25 72 226 102675 117902 0.241 0.851 -100 1
493576 10 -0.194713473 -2.061 110 530 555 259 46 310 310 334 181 54 55 30 0 1227 1295 412 31 309 309 328 108 32 100 99 0 0.240 0.248 0.270 0.243 2.861 0.228 0.160 425 2515 89 1138 1231 220 918 245 986 236052 550477 1.221 8.954 0 0
493578 18 0.516857929 -2.311 95 534 553 243 43 299 299 327 222 67 52 18 0 1455 1461 428 29 289 289 302 120 39 100 98 0 0.202 0.217 0.245 0.209 2.637 0.201 0.203 315 1915 90 1401 1426 235 1166 254 1172 174347 460182 1.018 9.658 0 0
493580 26 -0.028089214 -0.704 100 1186 1271 515 40 303 303 322 168 52 97 91 0 1747 1789 632 35 309 309 320 102 31 100 99 0 0.614 0.654 0.634 0.616 1.906 0.647 0.642 351 2108 95 2321 2448 883 1438 968 1480 446038 627830 5.649 14.402 0 0
493582 34 -2.322811413 0.930 85 3362 3490 1297 37 280 280 304 167 54 100 100 0 1898 2004 795 39 280 280 293 103 35 98 98 0 1.905 1.862 1.882 1.967 1.716 1.872 0.854 258 1544 92 4700 4934 3082 1618 3210 1724 900529 517095 19.078 16.612 0 0
493584 42 -0.570711728 1.241 100 6755 6926 2854 41 266 266 290 161 55 100 100 0 3011 3026 1431 47 265 265 275 103 37 97 95 0 2.363 2.412 2.491 2.646 1.926 2.427 0.851 321 2105 96 9235 9421 6489 2746 6660 2761 2223379 971305 41.217 26.709 0 0
493586 2 0.683112736 1.677 100 808 1518 1884 124 242 242 265 154 58 72 58 0 274 745 1072 143 97 97 178 198 111 49 37 0 3.198 1.969 1.922 2.365 3.689 1.898 0.821 316 2216 100 743 1924 566 177 1276 648 479641 235486 8.136 2.864 -100 1
493588 10 0.845453115 0.438 100 1047 1153 510 44 306 306 336 194 57 93 85 0 854 948 422 44 307 307 325 115 35 96 89 0 1.355 1.321 1.417 1.338 2.565 1.521 0.400 321 1975 91 1288 1488 741 547 847 641 370088 304311 4.211 5.417 0 0

Total number of rows: 24960

Table truncated, full table size 5672 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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