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Sample GSM132370 Query DataSets for GSM132370
Status Public on Aug 30, 2006
Title Exp. #24, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #2* REVERSED BEFORE P/C vs Fixed Nuclea
Sample type genomic
 
Channel 1
Source name DNA prepared from IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep.
Organism Saccharomyces cerevisiae
Characteristics DNA prepared from IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep.
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.
Organism Saccharomyces cerevisiae
Characteristics "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #24, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #2* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*
Data processing Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 28, 2006
Last update date Aug 29, 2006
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-843-3229
URL http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml
Organization name University of North Carolina at Chapel Hill
Department Biology
Lab Jason Lieb
Street address 203 Fordham Hall
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL4182
Series (2)
GSE5650 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- ORF-INT enrichment
GSE5662 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- ALL Arrays

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high LOG_RAT2N_MEDIANs imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
LOG_RAT2N_MEDIAN Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN
1 252 284 104 74 148 210 253 281 106 74 149 207 0 0 52 81 22 12 100 100 98 100 358 356 .705 1.419 1.389 1.397 1.441 1.347 52 370 1.36 .89 90 840 16720 95 104 79 88 0 158 41 117 .788 156 115 1.269 .772 -.343 -.374
2 1581 3801 103 73 1478 3728 1849 4262 105 75 1746 4189 0 0 904 2065 19 16 100 100 100 100 5206 5935 .396 2.522 2.399 2.745 2.442 1.572 80 515 2.493 .98 110 1020 16710 93 104 96 107 0 2112 41 2071 1.401 2368 2327 .714 1.333 .487 .415
3 2204 10944 104 75 2100 10869 2295 11367 106 76 2191 11292 0 0 451 2363 18 12 100 100 100 100 12969 13483 .193 5.176 5.154 5.17 5.166 1.132 52 341 5.249 .98 90 1190 16710 94 103 114 123 0 6080 42 6038 2.875 6315 6273 .348 2.863 1.524 1.518
4 1424 5224 103 75 1321 5149 1414 5382 105 75 1311 5307 0 0 520 1918 16 10 100 100 100 100 6470 6618 .257 3.898 4.048 4.05 3.78 1.431 52 303 3.918 .98 80 1370 16700 94 102 133 141 0 2902 42 2861 2.165 2990 2948 .462 2.249 1.115 1.169
5 1745 5504 104 75 1641 5429 2079 6678 106 77 1975 6603 0 0 956 2875 15 12 100 100 100 100 7070 8578 .302 3.308 3.343 3.622 3.2 1.552 80 461 3.259 .99 110 1550 16710 93 104 149 160 0 3058 42 3016 1.838 3710 3668 .544 1.857 .878 .893
6 967 11070 104 75 863 10995 1187 14065 106 78 1083 13990 0 0 492 5938 16 16 100 100 100 100 11858 15073 .078 12.74 12.918 12.676 12.588 1.424 80 477 12.805 .98 110 1720 16690 91 102 166 177 0 6150 42 6108 7.078 7814 7772 .141 7.177 2.823 2.843
7 2014 4805 103 73 1911 4732 2574 5986 104 75 2471 5913 0 0 1132 2623 15 13 100 100 100 100 6643 8384 .404 2.476 2.393 2.719 2.569 1.369 80 420 2.444 .99 100 1910 16700 93 103 186 196 0 2669 41 2629 1.376 3326 3285 .727 1.329 .46 .411
8 270 441 107 76 163 365 274 426 109 79 167 350 0 0 41 104 18 18 100 100 100 100 528 517 .447 2.239 2.096 2.224 2.282 1.306 32 215 2.336 .93 70 2060 16690 93 100 202 209 0 245 42 203 1.244 237 194 .804 1.164 .315 .22
9 1454 5630 103 73 1351 5557 1110 5430 105 75 1007 5357 0 0 1268 4751 18 14 97 100 97 100 6908 6364 .243 4.113 5.32 4.591 4.167 1.739 120 634 3.988 .98 130 2240 16700 91 104 217 230 0 3128 41 3087 2.285 3017 2976 .438 2.955 1.192 1.563
10 209 256 104 75 105 181 203 253 109 82 99 178 0 0 39 57 27 44 100 100 92 94 286 277 .58 1.724 1.798 1.756 1.784 1.389 52 317 1.743 .88 90 2410 16700 93 102 236 245 0 142 42 101 .958 141 99 1.044 .999 -.062 -.002
11 1795 7145 111 82 1684 7063 1901 7246 118 100 1790 7164 0 0 473 1356 40 73 100 100 100 100 8747 8954 .238 4.194 4.002 4.44 4.084 1.46 52 348 4.202 .97 90 2580 16690 92 101 253 262 0 3969 46 3924 2.33 4026 3980 .429 2.223 1.22 1.153
12 3373 11419 107 78 3266 11341 3682 11940 108 82 3575 11862 0 0 1048 1969 19 22 100 100 100 100 14607 15437 .288 3.472 3.318 3.892 3.414 1.71 52 358 3.364 .98 90 2760 16690 92 101 271 280 0 6344 43 6301 1.929 6633 6590 .518 1.843 .948 .882
13 2082 8426 105 75 1977 8351 2185 8594 109 89 2080 8519 0 0 525 1300 28 72 100 100 100 100 10328 10599 .237 4.224 4.096 4.508 4.093 1.446 52 363 4.094 .98 90 2930 16690 92 101 288 297 0 4681 42 4639 2.347 4774 4733 .426 2.275 1.231 1.186
14 2035 15937 106 78 1929 15859 2228 17298 109 86 2122 17220 0 0 658 4068 22 59 98 100 98 100 17788 19342 .122 8.221 8.115 8.52 8.048 1.365 52 360 8.159 .97 90 3100 16690 92 101 305 314 0 8854 43 8811 4.567 9610 9567 .219 4.508 2.191 2.173
15 2827 11397 108 79 2719 11318 3024 11763 109 79 2916 11684 0 0 729 2164 16 10 100 100 100 100 14037 14600 .24 4.163 4.007 4.41 4.043 1.491 52 375 4.129 .98 90 3280 16690 92 101 323 332 0 6332 44 6288 2.313 6535 6491 .432 2.226 1.209 1.154
16 2648 6205 107 76 2541 6129 2359 6270 109 77 2252 6194 0 0 1732 744 15 11 100 100 100 100 8670 8446 .415 2.412 2.75 2.61 2.762 1.355 52 299 2.2 .81 80 3450 16690 93 101 341 349 0 3447 42 3405 1.34 3483 3441 .746 1.528 .422 .612
17 2955 7634 109 77 2846 7557 2969 8194 109 78 2860 8117 0 0 679 1789 14 11 100 100 100 100 10403 10977 .377 2.655 2.838 2.647 2.672 1.264 52 305 2.698 .98 80 3620 16690 93 101 358 366 0 4241 43 4198 1.475 4552 4509 .678 1.577 .561 .657
18 800 4748 109 78 691 4670 822 4725 110 81 713 4647 0 0 208 951 16 35 100 100 100 100 5361 5360 .148 6.758 6.518 7.119 6.409 1.356 52 292 6.885 .95 80 3820 16690 93 101 378 386 0 2638 43 2594 3.755 2625 2582 .266 3.621 1.909 1.856
19 2786 11768 108 80 2678 11688 2857 12128 110 82 2749 12048 0 0 541 1395 16 19 100 100 100 100 14366 14797 .229 4.364 4.383 4.46 4.289 1.272 52 319 4.357 .98 80 3990 16680 92 100 395 403 0 6538 44 6493 2.425 6738 6693 .412 2.435 1.278 1.284
20 4620 1436 109 81 4511 1355 4983 1550 113 85 4874 1469 0 0 1471 305 61 57 100 100 100 100 5866 6343 3.329 .3 .301 .319 .306 1.347 52 286 .282 .97 80 4160 16690 93 101 412 420 0 798 45 753 .167 861 816 5.992 .167 -2.583 -2.578

Total number of rows: 16896

Table truncated, full table size 3828 Kbytes.




Supplementary data files not provided
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