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Sample GSM132377 Query DataSets for GSM132377
Status Public on Aug 30, 2006
Title Exp. #32, ORF enr. Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED ...
Sample type genomic
 
Channel 1
Source name Sonicated s288C Genomic DNA, Amplified Date of Experiment
Organism Saccharomyces cerevisiae
Characteristics Sonicated s288C Genomic DNA, Amplified Date of Experiment
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED BEFORE P/C, as)
Organism Saccharomyces cerevisiae
Characteristics Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED BEFORE P/C, as)
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Experiment Name: Exp. #32, ORF enr. Fixed Nuclear Extract (1% 30 min, same as jdl_g_112J sample but REVERSED BEFORE P/C, as) vs S288C Genomic DNA The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA WERE REVERSED prior to Phenol Chloroform prep Old Chan2 desc.: REVERSED Input from HH3 Lys4meth WT IP #2+3 after debris clearing spin
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 GPL4184
Series (2)
GSE5649 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- ORF 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 1223 2091 89 94 1134 1997 1267 2184 96 118 1178 2090 0 0 322 572 57 175 100 100 100 100 3131 3268 .568 1.761 1.774 1.769 1.753 1.247 120 612 1.783 .97 130 2070 16450 97 110 114 127 0 1209 54 1154 1.018 1262 1208 .982 1.026 .026 .036
2 4712 8708 93 101 4619 8607 4779 9042 113 151 4686 8941 0 0 656 1825 100 221 100 100 100 100 13226 13627 .537 1.863 1.908 1.815 1.905 1.327 156 599 1.939 .97 150 2250 16450 96 111 131 146 0 5034 58 4975 1.077 5227 5168 .928 1.103 .107 .141
3 7899 17881 96 100 7803 17781 8217 18052 109 129 8121 17952 0 0 1364 2751 82 147 100 100 100 100 25584 26073 .439 2.279 2.211 2.304 2.266 1.218 156 686 2.272 .97 150 2430 16430 94 109 149 164 0 10336 58 10278 1.317 10435 10377 .759 1.278 .397 .354
4 111 119 97 99 14 20 102 104 104 107 5 5 0 0 34 46 66 74 6 11 1 3 34 10 .7 1.429 1 1.553 1.682 3.289 80 329 1.188 .88 100 2600 16430 97 107 169 179 -100 69 57 12 .826 60 3 1.211 .578 -.276 -.791
5 5992 11820 94 97 5898 11723 6145 11908 102 104 6051 11811 0 0 1111 1944 70 57 100 100 100 100 17621 17862 .503 1.988 1.952 2.017 1.982 1.209 156 705 2.017 .96 150 2770 16430 94 109 183 198 0 6832 56 6776 1.149 6883 6827 .87 1.128 .2 .174
6 100 105 97 101 3 4 99 103 121 174 2 2 0 0 16 24 292 943 0 0 0 0 7 4 .75 1.333 1 1.347 1.394 3.511 80 378 6.517 .17 100 2950 16420 96 106 204 214 -100 61 58 2 .771 60 1 1.298 .578 -.376 -.791
7 8364 17889 104 112 8260 17777 8538 18750 181 538 8434 18638 0 0 1230 3321 568 2472 100 100 100 99 26037 27072 .465 2.152 2.21 2.124 2.185 1.342 120 510 2.254 .96 130 3120 16440 96 109 219 232 0 10340 65 10276 1.244 10838 10773 .804 1.277 .315 .353
8 1423 2739 104 112 1319 2627 1390 2743 150 358 1286 2631 0 0 509 1006 443 1839 95 75 80 20 3946 3917 .502 1.992 2.046 2.001 1.94 1.28 120 478 2.213 .95 120 3300 16420 95 107 238 250 0 1583 65 1518 1.151 1586 1521 .869 1.183 .203 .242
9 8445 18714 100 106 8345 18608 8480 18719 104 115 8380 18613 0 0 1043 2402 38 59 100 100 100 100 26953 26993 .448 2.23 2.221 2.229 2.248 1.099 156 611 2.248 .98 150 3480 16430 94 109 254 269 0 10817 61 10756 1.289 10820 10759 .776 1.284 .366 .361
10 1048 1853 103 107 945 1746 1038 1904 109 119 935 1797 0 0 366 626 71 88 99 99 98 99 2691 2732 .541 1.848 1.922 1.881 1.831 1.383 120 459 1.892 .94 120 3640 16420 95 107 272 284 0 1071 62 1009 1.068 1101 1039 .936 1.111 .095 .152
11 3463 6720 99 104 3364 6616 3509 6826 123 269 3410 6722 0 0 520 957 229 2657 100 100 100 94 9980 10132 .508 1.967 1.971 1.972 1.966 1.167 120 564 2.02 .94 130 3830 16410 93 106 290 303 0 3884 60 3824 1.137 3946 3886 .88 1.139 .185 .188
12 8174 17585 101 105 8073 17480 8318 18071 122 285 8217 17966 0 0 1197 2750 230 2755 100 100 100 100 25553 26183 .462 2.165 2.186 2.16 2.169 1.134 120 525 2.423 .9 130 4000 16410 93 106 307 320 0 10165 61 10104 1.252 10446 10385 .799 1.264 .324 .338
13 5782 12393 104 109 5678 12284 5892 12535 107 122 5788 12426 0 0 638 1489 23 136 100 100 100 100 17962 18214 .462 2.163 2.147 2.16 2.179 1.092 120 528 2.229 .95 130 4170 16420 94 107 324 337 0 7164 63 7101 1.251 7246 7183 .8 1.241 .323 .311
14 6331 13337 104 106 6227 13231 6657 13604 105 110 6553 13498 0 0 1818 3479 14 29 100 100 100 100 19458 20051 .471 2.125 2.06 2.195 2.108 1.541 120 563 2.131 .96 130 4350 16410 93 106 342 355 0 7709 61 7648 1.228 7864 7802 .814 1.191 .297 .252
15 4726 9197 103 104 4623 9093 4876 9492 104 108 4773 9388 0 0 1102 2608 15 28 100 100 100 100 13716 14161 .508 1.967 1.967 1.897 2.007 1.534 120 538 2.059 .96 130 4520 16410 93 106 359 372 0 5316 60 5256 1.137 5487 5427 .88 1.137 .185 .185
16 3661 6650 105 106 3556 6544 3699 6819 105 109 3594 6713 0 0 632 1587 14 23 100 100 100 100 10100 10307 .543 1.84 1.868 1.774 1.901 1.435 120 516 1.962 .94 130 4690 16410 93 106 376 389 0 3844 61 3783 1.064 3942 3880 .94 1.08 .089 .111
17 6011 11723 107 112 5904 11611 6220 11959 132 140 6113 11847 0 0 1044 1554 186 170 100 100 100 100 17515 17960 .508 1.967 1.938 2.003 1.934 1.311 120 463 1.973 .95 120 4860 16400 93 105 394 406 0 6776 65 6712 1.137 6913 6848 .88 1.12 .185 .164
18 5832 11734 107 110 5725 11624 6313 12544 130 137 6206 12434 0 0 1454 3083 180 165 100 100 100 100 17349 18640 .493 2.03 2.004 1.997 2.054 1.389 120 494 2.099 .96 120 5020 16400 93 105 410 422 0 6783 64 6719 1.174 7251 7187 .852 1.158 .231 .212
19 5544 10601 106 110 5438 10491 5716 11069 116 136 5610 10959 0 0 1371 2789 62 137 100 100 100 100 15929 16569 .518 1.929 1.953 1.922 1.945 1.611 120 523 1.987 .95 120 5210 16400 93 105 429 441 0 6128 64 6064 1.115 6398 6335 .897 1.129 .157 .175
20 3357 5844 105 112 3252 5732 3585 6327 126 164 3480 6215 0 0 894 1647 89 187 100 100 100 100 8984 9695 .567 1.763 1.786 1.739 1.752 1.582 120 464 1.813 .95 120 5380 16400 93 105 446 458 0 3378 65 3313 1.019 3657 3592 .982 1.032 .027 .046

Total number of rows: 16512

Table truncated, full table size 3741 Kbytes.




Supplementary data files not provided
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