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Sample GSM132347 Query DataSets for GSM132347
Status Public on Aug 30, 2006
Title Exp. #10, Intergenic enrichment. Fixed Whole Extract (1% 15 min) vs Whole Extract Nagy 4-25-02
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 Extract: Whole Fixed Yeast (1% 15 min) CSH Prep (P/C), Amplified Nagy 4-25
Organism Saccharomyces cerevisiae
Characteristics Extract: Whole Fixed Yeast (1% 15 min) CSH Prep (P/C), Amplified Nagy 4-25
Extracted molecule genomic DNA
Label Cy5
 
 
Description Extract: Whole Fixed Yeast (1% 15 min) CSH Prep (P/C), Amplified Nagy 4-25 vs. S288C yeast OD 1, No Fix, CSH prep (P/C), Amplified
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
1 524 491 221 247 303 244 529 477 224 248 308 230 0 0 97 92 36 37 100 100 100 96 547 538 1.242 .805 .747 .791 .923 1.462 32 204 .812 .85 70 1550 17340 81 88 91 98 0 571 287 284 .936 555 267 1.068 .868 -.095 -.204
2 5288 4753 245 275 5043 4478 5614 4872 921 1964 5369 4597 0 0 1048 869 3990 9622 82 0 0 0 9521 9966 1.126 .888 .856 .894 .884 1.269 52 383 2.45 .93 90 1720 17340 80 89 107 116 0 5527 320 5207 1.033 5665 5345 .969 .996 .046 -.006
3 7036 4101 361 363 6675 3738 7901 4330 481 455 7540 3967 0 0 2629 1459 616 658 100 100 98 92 10413 11507 1.786 .56 .526 .57 .537 1.414 52 321 .549 .96 80 1900 17340 81 89 126 134 0 4769 422 4347 .651 5035 4613 1.536 .612 -.619 -.709
4 3670 2173 741 576 2929 1597 3657 2161 758 607 2916 1585 0 0 929 494 253 181 100 100 100 100 4526 4501 1.834 .545 .544 .549 .541 1.269 52 314 .532 .97 80 2080 17340 81 89 144 152 0 2527 670 1857 .634 2513 1843 1.577 .632 -.657 -.662
5 6093 6715 740 583 5353 6132 6349 6902 802 631 5609 6319 0 0 982 1292 324 228 100 100 100 100 11485 11928 .873 1.146 1.127 1.135 1.154 1.249 52 308 1.181 .96 80 2260 17340 81 89 162 170 0 7808 678 7130 1.332 8026 7348 .751 1.31 .414 .39
6 8356 6695 647 526 7709 6169 8456 6662 741 597 7809 6136 0 0 1269 1128 340 249 100 100 100 100 13878 13945 1.25 .8 .786 .799 .798 1.243 52 305 .8 .97 80 2430 17340 81 89 179 187 0 7785 612 7173 .931 7747 7135 1.075 .914 -.104 -.13
7 5740 5078 421 384 5319 4694 5819 4793 455 403 5398 4409 0 0 1657 1631 152 102 100 100 100 100 10013 9807 1.133 .882 .817 .896 .827 1.578 52 363 .882 .92 90 2600 17340 80 89 195 204 0 5905 447 5458 1.026 5573 5127 .975 .95 .037 -.074
8 1872 1602 378 360 1494 1242 1910 1554 397 395 1532 1194 0 0 671 555 114 336 100 100 100 84 2736 2726 1.203 .831 .779 .84 .822 1.35 52 304 .913 .84 80 2780 17340 81 89 214 222 0 1863 419 1444 .967 1807 1388 1.034 .906 -.049 -.142
9 3684 5049 369 344 3315 4705 3472 4672 403 383 3103 4328 0 0 1324 1387 139 294 100 100 100 100 8020 7431 .705 1.419 1.395 1.509 1.346 1.679 52 360 1.346 .9 90 2960 17340 80 89 231 240 0 5871 400 5471 1.65 5433 5033 .606 1.622 .723 .698
10 1223 1169 443 406 780 763 1038 932 475 442 595 526 0 0 673 1006 192 158 77 76 62 58 1543 1121 1.022 .978 .884 .793 .829 1.962 80 404 1.294 .78 100 3150 17350 81 91 250 260 -100 1359 472 887 1.137 1084 612 .879 1.028 .186 .04
11 5338 4493 723 600 4615 3893 4780 3849 718 622 4057 3249 0 0 2117 1882 160 143 100 100 100 100 8508 7306 1.185 .844 .801 .853 .784 1.434 52 282 .833 .92 80 3310 17340 81 89 267 275 0 5224 698 4527 .981 4476 3778 1.019 .931 -.028 -.103
12 12561 6094 646 558 11915 5536 12769 5843 617 553 12123 5285 0 0 2116 1494 245 211 100 100 100 100 17451 17408 2.152 .465 .436 .456 .457 1.222 52 298 .467 .97 80 3490 17340 81 89 285 293 0 7086 649 6437 .54 6794 6145 1.851 .507 -.888 -.98
13 5220 3178 307 305 4913 2873 5304 3244 411 372 4997 2939 0 0 1291 647 259 193 100 100 100 100 7786 7936 1.71 .585 .588 .594 .587 1.2 52 354 .56 .97 90 3660 17340 80 89 301 310 0 3695 355 3341 .68 3772 3417 1.471 .684 -.556 -.548
14 8735 5579 338 318 8397 5261 8948 5611 365 341 8610 5293 0 0 1942 863 144 129 100 100 100 100 13658 13903 1.596 .627 .615 .636 .617 1.261 52 314 .597 .96 80 3840 17340 81 89 320 328 0 6487 370 6117 .729 6524 6155 1.373 .715 -.457 -.484
15 6702 6909 389 359 6313 6550 6656 7033 387 365 6267 6674 0 0 1261 1708 85 71 100 100 100 100 12863 12941 .964 1.038 1.065 1.019 1.026 1.26 52 320 1.077 .97 80 4020 17340 81 89 338 346 0 8034 417 7616 1.206 8178 7760 .829 1.238 .271 .308
16 4537 3092 297 305 4240 2787 4711 3094 322 315 4414 2789 0 0 739 383 89 68 100 100 100 100 7027 7203 1.521 .657 .632 .664 .628 1.27 52 298 .646 .97 80 4190 17340 81 89 355 363 0 3595 355 3241 .764 3598 3243 1.308 .735 -.388 -.445
17 3898 3247 262 278 3636 2969 4118 3520 266 284 3856 3242 0 0 709 869 79 50 100 100 100 100 6605 7098 1.225 .817 .841 .771 .839 1.375 52 295 .846 .97 80 4370 17340 81 89 373 381 0 3776 323 3452 .949 4093 3770 1.053 .978 -.075 -.033
18 2441 1966 263 278 2178 1688 2414 1870 266 282 2151 1592 0 0 661 437 73 50 100 100 100 100 3866 3743 1.29 .775 .74 .785 .817 1.241 52 363 .77 .94 90 4540 17340 80 89 389 398 0 2286 323 1963 .901 2174 1851 1.11 .861 -.15 -.217
19 7105 6691 263 273 6842 6418 7224 6762 283 286 6961 6489 0 0 1750 2042 220 94 100 100 100 100 13260 13450 1.066 .938 .932 .909 .922 1.27 52 391 .988 .96 90 4720 17340 80 89 407 416 0 7780 317 7463 1.091 7863 7545 .917 1.084 .125 .116
20 2072 1577 265 276 1807 1301 2057 1523 266 280 1792 1247 0 0 365 291 39 42 100 100 100 100 3108 3039 1.389 .72 .696 .72 .708 1.188 52 289 .714 .98 80 4890 17340 81 89 425 433 0 1834 321 1513 .837 1771 1450 1.194 .809 -.256 -.306

Total number of rows: 16896

Table truncated, full table size 3779 Kbytes.




Supplementary data files not provided
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