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Sample GSM562242 Query DataSets for GSM562242
Status Public on Jul 16, 2010
Title Pol2 IP from wt cells 120 min 37C heat shock [time course 1]
Sample type other
 
Channel 1
Source name Pol2 IP
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741 (WT)
genotype: wt
stress: 37C heat shock
time: 120 min
antibody: anti-Rpb3 monoclonal antibody (Neoclone; catalog# W0012)
Extracted molecule genomic DNA
Extraction protocol Chromatin associated with the target epitope was immunoprecipitated from mononucleosomal cell extract and amplified by TLAD.
Label Cy3-dCTP
Label protocol 3 ul of amplified DNA was combined with 20 ul random octamers from the Invitrogen BioPrime Labeling Kit and nuclease-free water to a volume of 41 ul. This was boiled for 5 minutes at 100C, then incubated on ice for 5 minutes. 5 ul of a low-C dNTP mix (25 mM dATP, 15 mM dCTP, 25 mM dGTP and 25 mM dTTP) and 3 ul of 1 mM Cy3-dCTP (for IP) or Cy5-dCTP (for input) were added, along with 1 ul of exo- Klenow fragment DNA polymerase (from the BioPrime kit), and the samples were incubated for 2.5 hours at 37C. IP and input probes were combined and brought up to 500 ul volume with water in a YM-30 Microcon column, and spun at 14,000 x g until the volume reduced to <50 ul. Water was added and the spin was repeated twice, with the final volume at 37.5 ul. At this stage, samples were labeled and ready for hybridization onto Agilent 44K arrays.
 
Channel 2
Source name input
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741 (WT)
genotype: wt
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-dCTP
Label protocol 3 ul of amplified DNA was combined with 20 ul random octamers from the Invitrogen BioPrime Labeling Kit and nuclease-free water to a volume of 41 ul. This was boiled for 5 minutes at 100C, then incubated on ice for 5 minutes. 5 ul of a low-C dNTP mix (25 mM dATP, 15 mM dCTP, 25 mM dGTP and 25 mM dTTP) and 3 ul of 1 mM Cy3-dCTP (for IP) or Cy5-dCTP (for input) were added, along with 1 ul of exo- Klenow fragment DNA polymerase (from the BioPrime kit), and the samples were incubated for 2.5 hours at 37C. IP and input probes were combined and brought up to 500 ul volume with water in a YM-30 Microcon column, and spun at 14,000 x g until the volume reduced to <50 ul. Water was added and the spin was repeated twice, with the final volume at 37.5 ul. At this stage, samples were labeled and ready for hybridization onto Agilent 44K arrays.
 
 
Hybridization protocol Amplified ChIP and ChIP input were mixed, purified by microcon, and hybridized to the microarrays in Agilent hybridization buffer for 16 hours at 65 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 6.0 analysis software.
Description BY4741 cells were grown to an OD of 0.5 in YPD shaking at 200 rpm at room temperature (25 degrees C). An equal volume of YPD prewarmed to 49 degrees C was added to flasks, which were immediately transferred to a 37 degrees C incubator and incubated at the indicated times before harvesting. Cells were then crosslinked with formaldehyde (1%) and washed with water. Cells were sonicated to shear DNA to ~500 bp, and subjected to immunoprecipitation with 5 ul anti-Rpb3 monoclonal antibody. As a reference, DNA was obtained from the input sheared chromatin prior to antibody addition. The ChIP and reference samples were amplified via Round A Round B amplification and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 Agilent S.cerevisiae whole genome arrays.
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 Jul 01, 2010
Last update date Jul 16, 2010
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 GPL4131
Series (1)
GSE22675 RNA Polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

Data table header descriptions
ID_REF Probe ID
Block printing block
VALUE Block Normalized Log2 (635/532) 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
23152 1 -0.994809525 -1.139 55 14811 13047 3866 29 52 52 52 13 25 100 100 0 32577 29308 12228 41 75 75 75 10 13 100 100 0 0.454 0.445 0.436 0.519 2.111 0.397 0.895 95 8 90 47261 42228 14759 32502 12995 29233 1239451 2784228 999.615 2923.300 0 0
20038 1 -1.451809525 -1.596 55 14400 12318 4369 35 49 49 50 16 32 100 100 0 43453 39646 15178 38 60 60 67 23 34 100 100 0 0.331 0.310 0.314 0.303 1.499 0.299 0.955 96 37 91 57744 51855 14351 43393 12269 39586 1182547 3805974 766.750 1720.826 0 0
3144 1 -0.714809525 -0.859 50 4655 4295 1247 29 44 44 41 19 46 100 100 0 8423 7807 2872 36 58 58 57 14 24 100 100 0 0.551 0.549 0.557 0.572 1.311 0.517 0.943 90 8 88 12976 12000 4611 8365 4251 7749 386523 702667 223.895 553.571 0 0
41483 1 -2.152809525 -2.297 50 4160 3786 1124 29 42 42 46 17 36 100 100 0 20286 18609 7176 38 52 52 56 10 17 100 100 0 0.204 0.202 0.199 0.218 1.997 0.174 0.824 91 6 89 24352 22301 4118 20234 3744 18557 344568 1693404 220.000 1855.300 0 0
9912 1 -0.804809525 -0.949 55 13160 10959 4257 38 58 58 58 15 25 100 100 0 25351 23565 7452 31 54 54 60 21 35 100 100 0 0.518 0.464 0.491 0.418 1.724 0.470 0.920 97 13 96 38399 34412 13102 25297 10901 23511 1063037 2285826 726.733 1119.286 0 0
5093 1 -1.130809525 -1.275 55 3234 3121 908 29 40 40 40 13 32 100 100 0 7774 7313 2690 36 47 47 59 26 44 100 100 0 0.413 0.424 0.422 0.446 1.448 0.393 0.923 93 8 90 10921 10347 3194 7727 3081 7266 290216 680150 237.000 279.000 0 0
17702 1 -1.302809525 -1.447 55 3359 3038 1020 33 46 46 51 15 29 100 100 0 9092 8764 2913 33 61 61 65 14 21 100 100 0 0.367 0.344 0.352 0.331 1.634 0.333 0.921 96 13 80 12344 11695 3313 9031 2992 8703 291658 841360 199.133 621.357 0 0
35319 1 -1.331809525 -1.476 55 4594 3828 1652 43 45 45 51 25 49 100 100 0 12704 11500 4222 36 47 47 56 30 53 100 100 0 0.359 0.330 0.354 0.286 2.845 0.305 0.764 96 6 86 17206 15236 4549 12657 3783 11453 367453 1103955 151.080 381.467 0 0
21415 1 -0.893809525 -1.038 55 5777 5416 1703 31 45 45 48 11 22 100 100 0 11827 10884 4343 39 55 55 55 16 29 100 100 0 0.487 0.496 0.497 0.527 1.419 0.462 0.941 95 11 95 17504 16200 5732 11772 5371 10829 514555 1033998 488.000 676.813 0 0
18721 1 -1.319809525 -1.464 55 5661 4997 1707 34 53 53 53 16 30 100 100 0 15548 14225 4628 32 73 73 69 18 26 100 100 0 0.362 0.349 0.360 0.342 1.320 0.346 0.967 95 10 95 21083 19096 5608 15475 4944 14152 474676 1351357 309.000 786.444 0 0
15134 1 -1.390809525 -1.535 55 5142 5080 1617 31 57 57 55 19 34 100 100 0 14798 14244 5550 38 61 61 67 19 28 100 100 0 0.345 0.354 0.358 0.380 1.733 0.325 0.904 93 11 93 19822 19206 5085 14737 5023 14183 472422 1324711 264.474 746.158 0 0
12371 1 -1.013809525 -1.158 55 3893 3380 1274 37 47 47 46 9 19 100 100 0 8650 8159 2784 34 67 67 65 21 32 100 100 0 0.448 0.412 0.429 0.385 1.435 0.411 0.950 98 12 89 12429 11425 3846 8583 3333 8092 331285 799547 370.444 385.429 0 0
15527 1 -1.279809525 -1.424 55 3993 3543 1318 37 48 48 49 16 32 100 100 0 10648 10123 2938 29 65 65 65 14 21 100 100 0 0.373 0.347 0.355 0.319 1.411 0.354 0.945 95 10 95 14528 13553 3945 10583 3495 10058 336579 961721 218.375 718.429 0 0
38311 1 -1.455809525 -1.600 55 4011 3802 1155 30 48 48 48 10 20 100 100 0 12064 11484 4331 37 51 51 50 14 28 100 100 0 0.330 0.328 0.328 0.345 1.411 0.306 0.941 89 12 95 15976 15187 3963 12013 3754 11433 338401 1022050 375.400 816.714 0 0
36251 1 -1.097809525 -1.242 55 5104 4515 1570 34 49 49 50 14 28 100 100 0 12013 11617 3520 30 54 54 61 19 31 100 100 0 0.423 0.386 0.408 0.355 1.777 0.378 0.886 91 19 93 17014 16029 5055 11959 4466 11563 410888 1057175 318.929 608.211 0 0
3944 1 -0.842809525 -0.987 55 4704 4265 1848 43 58 58 66 31 46 100 100 0 9256 9211 3322 36 49 49 51 7 13 100 100 0 0.505 0.459 0.486 0.401 1.831 0.469 0.915 97 5 95 13853 13369 4646 9207 4207 9162 413677 893487 135.452 1308.571 0 0
17109 1 -1.007809525 -1.152 55 5965 5217 2008 38 45 45 44 22 50 100 100 0 13224 12901 4055 31 68 68 77 17 22 100 100 0 0.450 0.403 0.427 0.362 1.665 0.406 0.921 97 7 91 19076 18005 5920 13156 5172 12833 506043 1251387 235.136 754.353 0 0
42414 1 -1.064809525 -1.209 55 3289 3163 1110 35 45 45 42 14 33 100 100 0 7545 7121 2989 41 45 45 56 22 39 100 100 0 0.433 0.441 0.448 0.468 1.651 0.409 0.918 96 5 88 10744 10194 3244 7500 3118 7076 303628 683622 222.929 321.136 0 0
27484 1 -0.904809525 -1.049 55 5413 5028 1386 27 53 53 53 15 28 100 100 0 11153 10381 3412 32 64 64 66 11 16 100 100 0 0.483 0.482 0.487 0.494 1.627 0.447 0.878 90 13 95 16449 15292 5360 11089 4975 10317 452493 934267 331.667 937.727 0 0
12031 1 -0.615809525 -0.760 55 5315 4585 1585 34 43 43 45 9 20 100 100 0 8980 8497 2706 31 54 54 57 18 31 100 100 0 0.591 0.538 0.552 0.517 1.354 0.538 0.952 93 12 88 14198 12985 5272 8926 4542 8443 426427 790197 504.444 468.889 0 0

Total number of rows: 41775

Table truncated, full table size 9712 Kbytes.




Supplementary file Size Download File type/resource
GSM562242.gpr.gz 5.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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