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Sample GSM562232 Query DataSets for GSM562232
Status Public on Jul 16, 2010
Title Pol2 IP from rpb1-1 cells 60 min 37C heat shock [time course 2]
Sample type other
 
Channel 1
Source name Pol2 IP
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741 rpb1-1 (TS)
genotype: rpb1-1 mutant
stress: 37C heat shock
time: 60 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 rpb1-1 (TS)
genotype: rpb1-1 mutant
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 bearing a temperature-sensitive mutation in rpb1were 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 -0.302057518 -0.920 55 13893 12605 4068 32 40 40 42 7 16 100 100 0 26265 24150 9634 39 62 62 67 18 26 100 100 0 0.529 0.522 0.521 0.562 1.917 0.479 0.889 96 9 92 40056 36653 13853 26203 12565 24088 1210127 2318443 1794.714 1337.944 0 0
20038 1 -0.846057518 -1.464 55 11466 9995 3690 36 38 38 45 17 37 100 100 0 31588 29174 8866 30 66 66 67 25 37 100 100 0 0.363 0.342 0.341 0.321 1.407 0.346 0.943 92 22 95 42950 39065 11428 31522 9957 29108 919519 2683981 585.294 1164.280 0 0
3144 1 0.075942482 -0.542 55 3485 3234 1110 34 41 41 44 13 29 100 100 0 5065 4879 1645 33 49 49 48 11 22 100 100 0 0.687 0.661 0.640 0.640 1.467 0.657 0.937 92 6 82 8460 8023 3444 5016 3193 4830 297504 448861 245.385 439.182 0 0
41483 1 -0.519057518 -1.137 50 4335 4135 1358 32 43 43 47 12 25 100 100 0 9496 9060 3614 39 58 58 56 17 30 100 100 0 0.455 0.455 0.455 0.493 1.924 0.410 0.849 92 9 90 13730 13094 4292 9438 4092 9002 380427 833509 340.667 529.647 0 0
9912 1 0.114942482 -0.503 55 9231 8933 2503 28 49 49 49 11 22 100 100 0 13068 11949 4773 39 57 57 62 17 27 100 100 0 0.706 0.747 0.754 0.840 1.647 0.687 0.919 94 11 84 22193 20776 9182 13011 8884 11892 839732 1123223 807.636 699.235 0 0
5093 1 -0.165057518 -0.783 65 2262 2419 855 35 41 41 42 11 26 100 100 0 3869 3700 1568 42 48 48 48 9 18 100 98 0 0.581 0.651 0.620 0.735 1.978 0.657 0.748 96 15 82 6042 6030 2221 3821 2378 3652 232220 355192 216.091 405.778 0 0
17702 1 -0.583057518 -1.201 55 2402 2161 923 42 53 53 52 12 23 96 96 0 5463 4900 1774 36 63 63 60 12 20 100 100 0 0.435 0.436 0.467 0.416 2.598 0.408 0.748 98 7 93 7749 6945 2349 5400 2108 4837 211773 480244 175.750 403.333 0 0
35319 1 -0.492057518 -1.110 55 2808 2788 913 32 48 48 45 10 22 100 100 0 6020 6040 2494 41 64 64 62 9 14 100 100 0 0.463 0.459 0.444 0.476 1.488 0.413 0.874 89 6 89 8716 8716 2760 5956 2740 5976 248128 537584 274.300 664.222 0 0
21415 1 -0.118057518 -0.736 55 4610 4192 2136 50 46 46 48 12 25 100 100 0 7651 7391 2752 37 49 49 46 10 21 100 100 0 0.600 0.565 0.577 0.444 2.183 0.598 0.882 100 7 92 12166 11488 4564 7602 4146 7342 419175 739082 345.333 734.500 0 0
18721 1 -0.411057518 -1.029 55 5244 4616 1862 40 46 46 47 9 19 100 100 0 10677 10030 3732 37 71 71 69 23 33 100 100 0 0.490 0.459 0.489 0.417 2.359 0.436 0.830 95 11 96 15804 14529 5198 10606 4570 9959 438498 952897 507.667 433.087 0 0
15134 1 -0.614057518 -1.232 55 5009 4553 2196 48 50 50 55 21 38 98 97 0 11720 11431 3373 29 70 70 74 21 28 100 100 0 0.426 0.396 0.435 0.307 2.789 0.405 0.786 97 5 90 16609 15864 4959 11650 4503 11361 441633 1108851 214.190 540.810 0 0
12371 1 -0.158057518 -0.776 55 2759 2494 949 38 42 42 41 8 19 100 100 0 4720 4393 1470 33 66 66 63 18 28 100 100 0 0.584 0.567 0.601 0.522 1.896 0.561 0.887 98 7 92 7371 6779 2717 4654 2452 4327 244397 430516 306.625 240.556 0 0
15527 1 -0.361057518 -0.979 55 3108 2936 898 30 45 45 41 9 21 100 100 0 6087 5697 1798 31 49 49 63 48 76 100 100 0 0.507 0.512 0.514 0.526 1.552 0.493 0.907 92 12 96 9101 8539 3063 6038 2891 5648 270076 524148 321.667 117.375 0 0
38311 1 -0.611057518 -1.229 55 2721 2666 1050 39 37 37 42 17 40 100 100 0 6340 5864 2334 39 50 50 49 17 34 100 100 0 0.427 0.452 0.449 0.445 1.697 0.433 0.901 95 13 91 8974 8443 2684 6290 2629 5814 253301 557081 154.353 342.059 0 0
36251 1 -0.055057518 -0.673 50 3098 3159 975 30 40 40 40 8 20 100 100 0 4922 4850 1641 33 46 46 47 14 29 100 100 0 0.627 0.649 0.645 0.663 1.404 0.621 0.895 90 21 86 7934 7923 3058 4876 3119 4804 284338 436530 389.875 343.071 0 0
3944 1 0.184942482 -0.433 50 4036 4109 1419 34 61 61 60 15 25 100 100 0 5417 5402 1823 33 51 51 54 23 42 100 100 0 0.741 0.756 0.790 0.740 1.426 0.751 0.930 92 6 94 9341 9399 3975 5366 4048 5351 378019 496995 269.933 232.522 0 0
17109 1 0.021942482 -0.596 55 4919 4544 1726 37 45 45 47 16 34 100 100 0 7419 7027 2512 35 54 54 58 12 20 100 100 0 0.662 0.645 0.680 0.623 1.811 0.634 0.890 94 10 92 12239 11472 4874 7365 4499 6973 427131 660523 281.063 580.750 0 0
42414 1 -0.245057518 -0.863 55 2557 2393 1012 42 37 37 39 4 10 100 100 0 4626 4634 1588 34 44 44 52 24 46 100 100 0 0.550 0.513 0.525 0.438 2.346 0.516 0.870 96 5 87 7102 6946 2520 4582 2356 4590 229718 444875 588.500 190.917 0 0
27484 1 -0.398057518 -1.016 55 3810 3359 1400 41 47 47 52 19 36 100 100 0 7662 7542 2204 29 51 51 57 18 31 100 100 0 0.494 0.442 0.478 0.368 2.351 0.448 0.838 95 10 88 11374 10803 3763 7611 3312 7491 319138 716457 174.053 415.833 0 0
12031 1 -0.056057518 -0.674 55 3237 2918 1051 36 48 48 48 11 22 100 100 0 5137 4721 1611 34 48 48 51 17 33 100 100 0 0.627 0.614 0.629 0.584 1.629 0.609 0.913 94 9 90 8278 7543 3189 5089 2870 4673 274295 443801 260.909 274.706 0 0

Total number of rows: 41775

Table truncated, full table size 9535 Kbytes.




Supplementary file Size Download File type/resource
GSM562232.gpr.gz 5.7 Mb (ftp)(http) GPR
Processed data included within Sample table
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