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Sample GSM132361 Query DataSets for GSM132361
Status Public on Aug 30, 2006
Title Exp. #13, Intergenic enrichment. Fixed Whole Extract (1% 30 min) REVERSED AFTER P/C prep vs ...
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, Fixed, CSH Prep (P/C), Amplified
Organism Saccharomyces cerevisiae
Characteristics S288C yeast OD 1, Fixed, CSH Prep (P/C), Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Experiment Name: Exp. #13, Intergenic enrichment. Fixed Whole Extract (1% 30 min) REVERSED AFTER P/C prep vs Whole Extract, Nagy 02-05-02 Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.
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)
GSE5648 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- Intergenic 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 1515 1287 275 169 1240 1118 1311 1152 329 201 1036 983 0 0 902 746 256 172 82 93 72 75 2358 2019 1.109 .902 .949 .959 .814 2.446 80 425 .848 .89 100 880 16830 73 83 73 83 0 1589 209 1380 1.113 1422 1214 .898 1.171 .155 .228
2 5652 4264 286 168 5366 4096 6201 4669 318 186 5915 4501 0 0 1641 1418 205 120 98 99 97 97 9462 10416 1.31 .763 .761 .707 .779 2.029 156 597 .756 .92 140 1070 16850 73 87 90 104 0 5264 207 5057 .942 5764 5557 1.061 .939 -.086 -.09
3 9937 5656 275 159 9662 5497 10702 6135 281 162 10427 5976 0 0 2440 1346 59 33 100 100 100 100 15159 16403 1.758 .569 .573 .576 .582 1.461 156 542 .54 .93 140 1250 16840 72 86 108 122 0 6983 196 6786 .702 7574 7378 1.424 .708 -.51 -.499
4 4141 2838 268 150 3873 2688 3964 2961 490 309 3696 2811 0 0 2216 1590 1387 899 90 89 55 56 6561 6507 1.441 .694 .761 .667 .662 1.925 156 559 .677 .91 140 1430 16840 72 86 126 140 0 3504 185 3319 .857 3656 3470 1.167 .939 -.223 -.091
5 6498 5827 239 138 6259 5689 6927 6093 299 192 6688 5955 0 0 1384 1205 598 444 98 100 98 99 11948 12643 1.1 .909 .89 .93 .908 1.753 156 570 .886 .92 140 1600 16840 72 86 143 157 0 7194 170 7023 1.122 7522 7352 .891 1.099 .166 .137
6 12485 4630 230 134 12255 4496 13089 4890 235 148 12859 4756 0 0 2236 913 63 102 100 100 99 100 16751 17615 2.726 .367 .37 .371 .367 1.701 156 562 .341 .91 140 1780 16840 72 86 161 175 0 5716 165 5551 .453 6037 5872 2.208 .457 -1.143 -1.131
7 11442 8241 230 133 11212 8108 11800 8799 267 158 11570 8666 0 0 1619 1959 180 115 100 100 100 100 19320 20236 1.383 .723 .749 .676 .742 1.832 156 698 .724 .91 150 1950 16840 71 86 177 192 0 10174 164 10010 .893 10863 10699 1.12 .925 -.164 -.113
8 1969 1470 232 137 1737 1333 1625 1360 256 146 1393 1223 0 0 1413 890 158 67 82 100 71 97 3070 2616 1.303 .767 .878 1.024 .695 3.358 80 374 .66 .84 100 2110 16810 71 81 196 206 0 1815 169 1646 .947 1679 1510 1.055 1.084 -.078 .116
9 10694 9373 236 135 10458 9238 12286 10686 255 162 12050 10551 0 0 4004 3840 131 202 97 96 95 94 19696 22601 1.132 .883 .876 .861 .88 2.801 208 848 .889 .89 160 2300 16840 71 87 212 228 0 11572 167 11405 1.091 13193 13026 .917 1.081 .125 .112
10 2137 1648 241 143 1896 1505 2331 1688 269 158 2090 1545 0 0 1090 616 119 68 92 100 86 100 3401 3635 1.26 .794 .739 1.03 .73 2.959 52 260 .67 .81 80 2460 16810 72 80 232 240 0 2035 177 1858 .98 2084 1907 1.02 .913 -.029 -.132
11 3939 2844 230 132 3709 2712 4017 2954 258 185 3787 2822 0 0 798 663 189 265 99 96 99 96 6421 6609 1.368 .731 .745 .711 .735 1.954 156 685 .717 .87 150 2650 16840 71 86 247 262 0 3511 163 3348 .903 3647 3484 1.108 .92 -.148 -.12
12 11305 11308 224 127 11081 11181 11864 11712 241 166 11640 11585 0 0 1884 3070 160 234 100 100 100 100 22262 23225 .991 1.009 .995 .974 1.003 1.633 156 502 1.043 .89 140 2820 16840 72 86 265 279 0 13960 157 13804 1.246 14459 14302 .803 1.229 .317 .297
13 9588 4248 226 126 9362 4122 10137 4447 228 126 9911 4321 0 0 2206 962 33 19 100 100 100 100 13484 14232 2.271 .44 .436 .453 .44 2.217 156 474 .389 .85 140 2990 16840 72 86 282 296 0 5244 156 5089 .544 5490 5335 1.84 .538 -.879 -.894
14 13647 4937 225 124 13422 4813 14364 5293 230 129 14139 5169 0 0 4320 1586 50 36 100 100 100 100 18235 19308 2.789 .359 .366 .362 .352 2.65 156 510 .314 .86 140 3160 16840 72 86 299 313 0 6095 153 5942 .443 6535 6381 2.259 .451 -1.176 -1.148
15 5347 3780 227 128 5120 3652 6049 4078 246 148 5822 3950 0 0 3061 2262 93 88 99 99 98 99 8772 9772 1.402 .713 .678 .693 .708 1.866 156 590 .701 .93 140 3330 16840 72 86 316 330 0 4667 158 4509 .881 5035 4877 1.136 .838 -.183 -.256
16 3918 3286 224 124 3694 3162 4189 3638 234 141 3965 3514 0 0 1487 1539 68 88 96 98 96 95 6856 7479 1.168 .856 .886 .8 .887 1.909 156 495 .893 .9 140 3510 16850 73 87 334 348 0 4057 153 3904 1.057 4491 4338 .946 1.094 .08 .13
17 6265 5669 221 123 6044 5546 6913 6279 222 127 6692 6156 0 0 1684 1751 28 58 100 100 100 100 11590 12848 1.09 .918 .92 .877 .922 2.107 156 579 .93 .89 150 3680 16840 71 86 350 365 0 6999 152 6847 1.133 7752 7600 .883 1.136 .18 .184
18 6111 3485 223 122 5888 3363 6874 3757 227 125 6651 3635 0 0 3233 1669 48 29 99 100 98 100 9251 10286 1.751 .571 .547 .673 .542 2.603 156 655 .526 .91 150 3850 16830 70 85 367 382 0 4302 151 4152 .705 4638 4488 1.418 .675 -.504 -.568
19 5662 4844 227 125 5435 4719 5768 5352 243 135 5541 5227 0 0 3329 2893 103 51 99 100 99 99 10154 10768 1.152 .868 .943 .838 .862 2.203 156 546 .856 .93 140 4020 16840 72 86 385 399 0 5980 154 5826 1.072 6607 6453 .933 1.165 .1 .22
20 2153 3502 222 125 1931 3377 1363 2271 226 129 1141 2146 0 0 1518 2325 40 31 98 100 94 100 5308 3287 .572 1.749 1.881 2.03 1.647 2.115 156 516 1.726 .91 140 4200 16830 71 85 403 417 0 4323 154 4169 2.159 2804 2649 .463 2.322 1.11 1.215

Total number of rows: 16896

Table truncated, full table size 3861 Kbytes.




Supplementary data files not provided
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