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Sample GSM132363 Query DataSets for GSM132363
Status Public on Aug 30, 2006
Title Exp. #16, Intergenic enrichment. Fixed Whole Extract (1% 60 min, 30 mins @ 37 w/ProtK, P/C) 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 Extract: Whl Fixed Yst (1% 60min, break, 30mins @37 ProtK, then CSH P/C), Amped Nagy 4-25
Organism Saccharomyces cerevisiae
Characteristics Extract: Whl Fixed Yst (1% 60min, break, 30mins @37 ProtK, then CSH P/C), Amped Nagy 4-25
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Experiment Name: Exp. #16, Intergenic enrichment. Fixed Whole Extract (1% 60 min, 30 mins @ 37 w/ProtK, P/C) vs Whole Extract. Nagy 4-25-02
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 GPL4182
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
1 353 470 180 220 173 250 343 473 169 216 163 253 0 0 101 110 59 106 84 88 75 69 423 416 .692 1.445 1.552 1.57 1.477 1.775 52 311 1.334 .89 80 1050 16950 61 69 101 109 -100 307 144 163 .945 309 165 1.059 1.014 -.082 .021
2 3501 5799 188 224 3313 5575 3775 5989 185 235 3587 5765 0 0 984 914 59 113 100 100 100 100 8888 9352 .594 1.683 1.607 1.812 1.611 1.472 52 373 1.633 .97 90 1220 16960 61 70 117 126 0 3790 146 3644 1.1 3914 3768 .909 1.05 .137 .071
3 4321 6977 188 217 4133 6760 4757 7327 197 234 4569 7110 0 0 1152 1228 322 193 100 100 100 100 10893 11679 .611 1.636 1.556 1.723 1.579 1.366 32 233 1.649 .95 70 1400 16950 61 68 136 143 0 4560 142 4418 1.069 4789 4647 .935 1.017 .096 .024
4 2594 4406 193 217 2401 4189 2777 4356 177 209 2584 4139 0 0 683 861 58 81 100 100 100 100 6590 6723 .573 1.745 1.602 1.847 1.723 1.409 32 176 1.715 .97 60 1580 16950 62 68 155 161 0 2880 142 2738 1.14 2847 2705 .877 1.047 .189 .066
5 3464 6148 192 227 3272 5921 4070 6021 189 221 3878 5794 0 0 1662 3623 40 56 96 96 94 96 9193 9672 .553 1.81 1.494 1.917 1.515 2.649 52 308 2.027 .87 80 1760 16950 61 69 172 180 0 4018 148 3870 1.183 3935 3787 .845 .977 .242 -.034
6 5735 7372 195 223 5540 7149 6103 7740 197 223 5908 7517 0 0 1572 1674 32 38 100 100 100 100 12689 13425 .775 1.29 1.272 1.327 1.297 1.362 52 298 1.261 .96 80 1920 16960 62 70 188 196 0 4818 146 4673 .843 5059 4913 1.186 .832 -.246 -.266
7 4814 6423 198 226 4616 6197 4865 6355 204 237 4667 6129 0 0 1071 1004 51 129 100 100 100 100 10813 10796 .745 1.343 1.313 1.371 1.309 1.279 52 311 1.295 .96 80 2100 16960 62 70 206 214 0 4198 148 4050 .877 4154 4006 1.14 .858 -.189 -.22
8 388 469 194 217 194 252 381 458 195 219 187 241 0 0 77 95 29 34 100 100 98 100 446 428 .77 1.299 1.289 1.309 1.31 1.412 52 298 1.305 .89 80 2280 16950 61 69 224 232 0 307 142 165 .849 299 158 1.178 .842 -.236 -.248
9 6342 8427 198 226 6144 8201 6121 7894 200 229 5923 7668 0 0 2410 3053 28 38 100 100 100 100 14345 13591 .749 1.335 1.295 1.366 1.353 1.295 80 427 1.331 .97 100 2450 16960 61 71 240 250 0 5508 148 5360 .872 5159 5012 1.146 .846 -.197 -.241
10 403 500 198 215 205 285 400 503 200 217 202 288 0 0 47 75 28 40 100 100 100 100 490 490 .719 1.39 1.426 1.38 1.374 1.421 32 225 1.472 .82 70 2630 16950 61 68 259 266 0 327 141 186 .909 329 188 1.101 .932 -.138 -.102
11 3226 5337 205 220 3021 5117 3276 5381 205 219 3071 5161 0 0 533 893 29 35 100 100 100 100 8138 8232 .59 1.694 1.681 1.697 1.681 1.136 52 303 1.686 .97 80 2800 16950 61 69 276 284 0 3488 144 3344 1.107 3517 3373 .903 1.098 .147 .135
12 9617 10885 205 230 9412 10655 10671 12358 206 234 10466 12128 0 0 2504 3056 29 38 100 100 100 100 20067 22594 .883 1.132 1.159 1.127 1.168 1.557 52 353 1.14 .95 90 2970 16960 61 70 292 301 0 7114 150 6964 .74 8077 7927 1.352 .757 -.435 -.401
13 5413 6952 203 229 5210 6723 5270 6794 204 229 5067 6565 0 0 824 1180 29 39 100 100 100 100 11933 11632 .775 1.29 1.296 1.283 1.31 1.229 52 366 1.296 .96 90 3150 16960 61 70 310 319 0 4544 150 4394 .843 4441 4291 1.186 .847 -.246 -.24
14 7835 8994 204 225 7631 8769 8749 9125 205 226 8545 8900 0 0 2999 2236 30 38 100 100 100 100 16400 17445 .87 1.149 1.042 1.345 1.072 1.886 52 303 1.058 .94 80 3330 16950 61 69 329 337 0 5878 147 5731 .751 5964 5817 1.331 .681 -.413 -.555
15 5675 9960 203 223 5472 9737 5875 10223 204 226 5672 10000 0 0 1742 3033 28 36 100 100 100 100 15209 15672 .562 1.779 1.763 1.826 1.787 1.566 52 364 1.785 .96 90 3500 16960 61 70 345 354 0 6510 146 6364 1.163 6682 6536 .86 1.152 .218 .205
16 3968 7307 205 233 3763 7074 4080 7228 207 234 3875 6995 0 0 950 1216 30 38 100 100 100 100 10837 10870 .532 1.88 1.805 1.957 1.865 1.359 52 303 1.855 .96 80 3680 16950 61 69 364 372 0 4776 152 4624 1.229 4724 4572 .814 1.18 .297 .239
17 5156 11011 208 229 4948 10782 5435 11660 210 231 5227 11431 0 0 1105 1752 29 34 100 100 100 100 15730 16658 .459 2.179 2.187 2.225 2.118 1.252 52 308 2.159 .98 80 3850 16950 61 69 381 389 0 7197 150 7047 1.424 7621 7471 .702 1.429 .51 .515
18 1810 2185 210 237 1600 1948 1778 2106 212 237 1568 1869 0 0 500 690 30 34 98 100 98 100 3548 3437 .821 1.218 1.192 1.259 1.244 1.864 52 356 1.305 .91 90 4040 16960 61 70 399 408 0 1428 155 1273 .796 1376 1222 1.257 .779 -.33 -.36
19 6375 11191 217 239 6158 10952 7557 12369 216 242 7340 12130 0 0 2681 3527 30 37 100 100 98 100 17110 19470 .562 1.778 1.653 2.25 1.7 2.241 52 362 1.686 .96 90 4210 16950 60 69 416 425 0 7314 156 7158 1.162 8084 7928 .86 1.08 .217 .111
20 1435 5557 220 246 1215 5311 1460 5670 219 247 1240 5424 0 0 240 847 27 36 100 100 100 100 6526 6664 .229 4.371 4.374 4.418 4.427 1.289 52 299 4.496 .96 80 4380 16950 61 69 434 442 0 3632 161 3471 2.857 3706 3545 .35 2.859 1.514 1.515

Total number of rows: 16896

Table truncated, full table size 3856 Kbytes.




Supplementary data files not provided
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