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Sample GSM132351 Query DataSets for GSM132351
Status Public on Aug 30, 2006
Title Exp. #02, Neutral. Whole Extract vs Whole Extract Nagy 2-05-02
Sample type genomic
 
Channel 1
Source name S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified
Organism Saccharomyces cerevisiae
Characteristics S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified
Organism Saccharomyces cerevisiae
Characteristics S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description The DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees. Extract: Whole Unfixed vs Whole, Unfixed. Int Enr Nagy 2-05-02
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 GPL4183
Series (2)
GSE5651 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- Neutral 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 2029 1579 208 114 1821 1465 1223 1107 213 119 1015 993 0 0 1561 1296 58 65 99 100 99 99 3286 2008 1.243 .805 .978 .79 .8 2.11 120 681 .795 .87 130 1260 17370 55 68 109 122 0 2105 152 1953 1.073 1476 1324 .932 1.304 .101 .383
2 9717 8372 210 117 9507 8255 9790 8416 223 140 9580 8299 0 0 844 695 109 181 100 100 100 100 17762 17879 1.152 .868 .866 .869 .872 1.139 120 528 .847 .94 130 1430 17370 55 68 126 139 0 11163 156 11007 1.158 11221 11065 .864 1.155 .211 .208
3 10941 11353 211 116 10730 11237 12094 12373 285 231 11883 12257 0 0 3782 3679 647 677 93 98 92 96 21967 24140 .955 1.047 1.031 1.152 1.065 1.974 156 613 1.029 .93 140 1600 17370 55 69 143 157 0 15137 155 14983 1.396 16497 16343 .716 1.375 .482 .46
4 10571 6221 215 119 10356 6102 10728 6496 449 456 10513 6377 0 0 1527 1535 1432 1590 100 98 100 90 16458 16890 1.697 .589 .607 .566 .604 1.442 120 494 .594 .93 130 1780 17380 56 69 161 174 0 8295 159 8136 .786 8661 8503 1.273 .809 -.348 -.306
5 10873 7899 213 118 10660 7781 11381 8410 273 264 11168 8292 0 0 1914 1810 603 946 99 96 99 96 18441 19460 1.37 .73 .742 .698 .738 1.712 156 565 .719 .93 140 1950 17380 56 70 178 192 0 10532 157 10375 .973 11213 11056 1.028 .99 -.039 -.015
6 14030 12189 212 120 13818 12069 15430 13514 219 149 15218 13394 0 0 3747 3633 76 193 100 100 99 99 25887 28612 1.145 .873 .88 .851 .882 2.05 156 547 .864 .91 140 2120 17380 56 70 195 209 0 16252 160 16092 1.165 18019 17859 .859 1.174 .22 .231
7 12805 12955 217 122 12588 12833 14133 13897 234 155 13916 13775 0 0 3496 2767 97 133 100 100 100 100 25421 27691 .981 1.019 .99 1.084 .993 1.897 156 657 .977 .89 140 2290 17380 56 70 212 226 0 17273 163 17111 1.359 18529 18367 .736 1.32 .443 .4
8 3098 2520 220 127 2878 2393 3101 2688 245 180 2881 2561 0 0 1403 1424 147 292 100 91 97 85 5271 5442 1.203 .831 .889 .699 .783 3.034 80 358 .871 .79 100 2460 17400 60 70 231 241 0 3360 169 3191 1.109 3584 3415 .902 1.185 .149 .245
9 12222 13581 218 121 12004 13460 12615 13863 234 161 12397 13742 0 0 1825 1806 132 245 100 100 100 100 25464 26139 .892 1.121 1.108 1.131 1.119 1.274 156 801 1.11 .91 150 2640 17380 55 70 246 261 0 18108 161 17947 1.495 18484 18323 .669 1.478 .58 .564
10 2057 1748 225 124 1832 1624 1934 1674 239 156 1709 1550 0 0 717 606 144 123 100 100 100 100 3456 3259 1.128 .886 .907 .893 .93 1.748 52 291 .81 .77 90 2810 17400 60 69 266 275 0 2331 165 2165 1.182 2232 2067 .846 1.209 .241 .274
11 5728 3949 216 119 5512 3830 5941 4263 224 148 5725 4144 0 0 1262 1089 47 127 100 100 99 98 9342 9869 1.439 .695 .724 .675 .71 1.835 156 680 .677 .91 140 2980 17390 57 71 281 295 0 5265 159 5107 .926 5684 5525 1.079 .965 -.11 -.051
12 13209 11058 216 117 12993 10941 14024 12548 221 137 13808 12431 0 0 2787 3693 44 117 100 100 100 99 23934 26239 1.188 .842 .9 .744 .898 2.222 156 539 .88 .87 140 3160 17400 58 72 299 313 0 14744 156 14588 1.123 16731 16575 .891 1.2 .167 .263
13 7958 9621 215 118 7743 9503 8400 10820 226 156 8185 10702 0 0 1626 2926 74 285 100 99 100 96 17246 18887 .815 1.227 1.308 1.119 1.293 2.093 156 540 1.312 .9 140 3330 17400 58 72 316 330 0 12828 157 12671 1.636 14427 14269 .611 1.743 .711 .802
14 10726 11790 216 122 10510 11668 11912 13648 226 168 11696 13526 0 0 3453 4749 76 307 100 100 100 99 22178 25222 .901 1.11 1.156 1.02 1.176 2.174 120 440 1.187 .88 120 3510 17410 60 72 335 347 0 15720 163 15557 1.48 18197 18035 .676 1.542 .566 .625
15 8164 6602 216 121 7948 6481 8492 6778 228 139 8276 6657 0 0 2370 1884 133 102 100 100 100 100 14429 14933 1.226 .815 .804 .822 .817 1.641 120 502 .793 .91 120 3670 17400 59 71 351 363 0 8803 161 8641 1.087 9037 8876 .92 1.072 .121 .101
16 5454 4237 216 118 5238 4119 5994 4737 225 130 5778 4619 0 0 1824 1515 122 89 98 100 97 98 9357 10397 1.272 .786 .799 .776 .799 2.131 156 610 .766 .89 140 3850 17400 58 72 368 382 0 5649 157 5492 1.048 6316 6159 .954 1.066 .068 .092
17 8983 6135 216 117 8767 6018 9386 6862 218 125 9170 6745 0 0 2272 2154 29 64 100 100 100 100 14785 15915 1.457 .686 .736 .633 .73 1.98 120 455 .71 .88 130 4030 17410 59 72 386 399 0 8180 156 8024 .915 9149 8993 1.093 .981 -.128 -.028
18 9025 8707 219 117 8806 8590 9622 8519 225 127 9403 8402 0 0 2982 1723 60 72 100 100 97 100 17396 17805 1.025 .975 .894 1.065 .924 1.951 120 552 .884 .88 130 4200 17400 58 71 403 416 0 11609 156 11453 1.301 11359 11203 .769 1.191 .379 .253
19 9917 6768 224 121 9693 6647 11265 7981 244 158 11041 7860 0 0 3246 2789 111 149 100 100 100 97 16340 18901 1.458 .686 .712 .615 .705 2.183 120 528 .69 .89 120 4370 17410 60 72 421 433 0 9024 161 8863 .914 10641 10480 1.094 .949 -.129 -.075
20 5258 2829 222 119 5036 2710 5911 3212 229 132 5689 3093 0 0 1922 1129 49 76 100 100 100 100 7746 8782 1.858 .538 .544 .522 .542 1.936 120 475 .506 .87 120 4550 17410 60 72 439 451 0 3772 159 3613 .718 4283 4124 1.394 .725 -.479 -.464

Total number of rows: 16896

Table truncated, full table size 3850 Kbytes.




Supplementary data files not provided

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