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Sample GSM132354 Query DataSets for GSM132354
Status Public on Aug 30, 2006
Title Exp. #05, Neutral. 0.1 ng S288C Genomic DNA, amplified vs 50ng of same DNA, amplified
Sample type genomic
 
Channel 1
Source name Original S288C DNA (Derisi), 50 ng, Amplified
Organism Saccharomyces cerevisiae
Characteristics Original S288C DNA (Derisi), 50 ng, Amplified
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Original S288C DNA (Derisi), 0.1 ng, Amplified
Organism Saccharomyces cerevisiae
Characteristics Original S288C DNA (Derisi), 0.1 ng, Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description The purpose of this array was to rule out any amplification bias linked to concentration of input DNA. 0.1 ng of input genomic DNA was the lowest amount for which we could achieve robust amplification.
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)
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
1 922 1354 138 135 784 1219 814 1173 139 136 676 1038 0 0 320 530 19 19 100 100 100 100 2003 1714 .643 1.555 1.536 1.538 1.543 1.152 52 311 1.567 .99 90 2200 16990 82 91 154 163 0 915 91 824 1.051 793 701 .952 1.038 .071 .053
2 4909 7336 140 139 4769 7197 4898 7246 141 144 4758 7107 0 0 528 925 19 28 100 100 100 100 11966 11865 .663 1.509 1.494 1.505 1.498 1.078 52 364 1.514 .99 90 2370 16990 82 91 171 180 0 4957 94 4863 1.02 4896 4802 .981 1.009 .028 .013
3 8056 9731 135 139 7921 9592 8696 10432 137 141 8561 10293 0 0 1549 1978 19 27 100 100 100 100 17513 18854 .826 1.211 1.202 1.206 1.189 1.072 52 362 1.211 1 90 2550 16990 82 91 189 198 0 6575 94 6481 .818 7049 6955 1.222 .812 -.289 -.3
4 5903 6625 139 138 5764 6487 6331 7215 139 138 6192 7077 0 0 1325 1671 18 21 100 100 100 100 12251 13269 .889 1.125 1.143 1.111 1.133 1.087 52 358 1.142 .99 90 2730 16980 81 90 207 216 0 4476 93 4383 .76 4875 4782 1.315 .772 -.395 -.373
5 5778 7843 146 149 5632 7694 6741 9318 146 150 6595 9169 0 0 2253 2889 20 34 100 100 100 100 13326 15764 .732 1.366 1.39 1.442 1.394 1.387 80 402 1.351 .99 100 2900 16990 82 92 224 234 0 5299 101 5199 .923 6296 6195 1.083 .939 -.116 -.09
6 8909 13307 152 152 8757 13155 9713 14551 152 153 9561 14399 0 0 1753 3055 20 24 100 100 100 100 21912 23960 .666 1.502 1.506 1.484 1.527 1.119 52 358 1.507 .99 90 3070 16980 81 90 241 250 0 8991 103 8889 1.015 9832 9729 .985 1.018 .022 .025
7 7899 11156 148 150 7751 11006 8654 12642 148 150 8506 12492 0 0 2154 3531 19 23 100 100 100 100 18757 20998 .704 1.42 1.469 1.391 1.469 1.237 52 364 1.446 .99 90 3250 16980 81 90 259 268 0 7538 101 7436 .959 8542 8441 1.042 .992 -.06 -.011
8 1078 1597 146 143 932 1454 760 1102 146 144 614 959 0 0 737 1152 18 21 100 100 100 100 2386 1573 .641 1.56 1.562 1.605 1.561 1.271 80 403 1.561 .99 100 3430 16990 82 92 277 287 0 1079 97 982 1.054 745 648 .949 1.055 .076 .078
9 8941 10966 145 144 8796 10822 10103 12476 146 146 9958 12332 0 0 3347 3631 18 20 100 100 100 100 19618 22290 .813 1.23 1.238 1.347 1.256 1.465 80 394 1.203 .99 100 3610 16990 82 92 295 305 0 7409 97 7312 .831 8430 8332 1.203 .837 -.267 -.257
10 733 940 147 148 586 792 572 792 148 148 425 644 0 0 396 542 19 22 100 100 100 100 1378 1069 .74 1.352 1.515 1.328 1.353 1.252 80 383 1.36 .98 100 3790 16990 82 92 313 323 0 635 100 535 .913 535 435 1.095 1.024 -.131 .034
11 2976 3991 150 152 2826 3839 3173 4296 151 152 3023 4144 0 0 987 1229 19 23 100 100 100 100 6665 7167 .736 1.358 1.371 1.428 1.377 1.361 80 366 1.341 .99 100 3960 16990 82 92 330 340 0 2697 103 2594 .918 2903 2800 1.089 .926 -.124 -.111
12 9050 8653 150 154 8900 8499 10318 9382 152 156 10168 9228 0 0 2847 2525 25 30 100 100 100 100 17399 19396 1.047 .955 .908 .977 .948 1.157 80 416 .943 .99 100 4140 16990 82 92 348 358 0 5847 104 5743 .645 6339 6235 1.55 .613 -.632 -.706
13 5058 6243 155 164 4903 6079 5255 7330 188 204 5100 7166 0 0 3410 3372 330 313 90 100 84 96 10982 12266 .807 1.24 1.405 1.61 1.215 1.89 32 201 1.13 .98 70 4310 17010 85 92 366 373 0 4218 111 4107 .838 4953 4842 1.194 .949 -.255 -.075
14 7182 11359 154 157 7028 11202 7730 12541 156 159 7576 12384 0 0 1485 3058 24 29 100 100 100 100 18230 19960 .627 1.594 1.635 1.546 1.636 1.178 52 356 1.631 .99 90 4490 16980 81 90 383 392 0 7675 106 7569 1.077 8474 8368 .929 1.104 .107 .143
15 6118 10900 150 155 5968 10745 6214 11587 151 156 6064 11432 0 0 689 1769 24 24 100 100 100 100 16713 17496 .555 1.8 1.885 1.783 1.836 1.123 52 364 1.817 .99 90 4660 16980 81 90 400 409 0 7365 105 7260 1.217 7829 7724 .822 1.274 .283 .349
16 4060 3420 146 152 3914 3268 4607 3737 167 173 4461 3585 0 0 1520 1320 282 182 98 96 96 96 7182 8046 1.198 .835 .804 .821 .837 1.263 52 311 .836 .99 80 4830 16980 82 90 418 426 0 2311 103 2208 .564 2525 2422 1.773 .543 -.826 -.881
17 5118 6343 146 149 4972 6194 5466 6782 174 184 5320 6633 0 0 951 1312 280 202 100 100 100 100 11166 11953 .803 1.246 1.247 1.239 1.273 1.118 52 344 1.244 .99 90 5020 16990 82 91 436 445 0 4286 101 4185 .842 4582 4482 1.188 .842 -.249 -.247
18 4141 6059 142 145 3999 5914 4360 6481 141 149 4218 6336 0 0 962 1338 20 37 100 100 100 100 9913 10554 .676 1.479 1.502 1.487 1.487 1.114 52 343 1.472 .99 90 5190 16990 82 91 453 462 0 4094 98 3996 .999 4379 4281 1.001 1.015 -.001 .021
19 5956 8735 138 141 5818 8594 6397 9437 139 145 6259 9296 0 0 1141 2114 21 36 100 100 100 100 14412 15555 .677 1.477 1.485 1.447 1.517 1.143 52 360 1.501 .99 90 5370 16980 81 90 471 480 0 5902 95 5807 .998 6376 6281 1.002 1.004 -.003 .005
20 4267 3940 140 141 4127 3799 4501 4171 139 143 4361 4030 0 0 858 983 19 20 100 100 100 100 7926 8391 1.086 .921 .924 .902 .921 1.137 52 281 .931 .99 80 5550 16980 82 90 490 498 0 2662 95 2567 .622 2818 2723 1.608 .624 -.685 -.679

Total number of rows: 16896

Table truncated, full table size 3923 Kbytes.




Supplementary data files not provided

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