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Sample GSM132349 Query DataSets for GSM132349
Status Public on Aug 30, 2006
Title Exp. #17, Intergenic enrichment. Fixed Whole Extract (5% 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 (5% 15 min) CSH Prep (P/C), Amplified Nagy 4-25
Organism Saccharomyces cerevisiae
Characteristics Extract: Whole Fixed Yeast (5% 15 min) CSH Prep (P/C), Amplified Nagy 4-25
Extracted molecule genomic DNA
Label Cy5
 
 
Description Extract: Whole Fixed Yeast (5% 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
1 459 649 286 432 173 217 441 645 290 429 155 213 0 0 84 88 40 49 100 96 94 92 390 368 .797 1.254 1.374 1.275 1.28 1.806 52 291 1.314 .73 80 1720 16420 88 96 91 99 0 636 424 213 1.23 632 209 .813 1.347 .298 .43
2 5695 3131 290 436 5405 2695 5599 3139 290 438 5309 2703 0 0 1233 525 38 52 100 100 100 100 8100 8012 2.006 .499 .509 .502 .51 1.283 52 317 .476 .94 80 1890 16420 88 96 108 116 0 3070 427 2642 .489 3077 2650 2.046 .499 -1.033 -1.002
3 10094 10550 308 462 9786 10088 6489 3901 317 465 6181 3439 1 3 12064 16276 62 57 100 100 100 100 19874 9620 .97 1.031 .556 .686 .625 1.78 52 369 1.282 .89 90 2080 16420 87 96 126 135 0 10343 453 9890 1.011 3825 3372 .989 .545 .015 -.874
4 2426 1608 323 462 2103 1146 2413 1644 334 471 2090 1182 0 0 516 266 67 64 100 100 100 100 3249 3272 1.835 .545 .566 .546 .53 1.278 52 303 .518 .95 80 2240 16420 88 96 143 151 0 1576 453 1124 .534 1612 1159 1.872 .554 -.904 -.851
5 4858 4216 307 453 4551 3763 4881 4289 309 456 4574 3836 0 0 905 777 39 53 100 100 100 100 8314 8410 1.209 .827 .839 .822 .862 1.253 52 363 .824 .95 90 2420 16420 87 96 160 169 0 4133 444 3689 .811 4205 3761 1.234 .822 -.303 -.282
6 10171 6224 378 530 9793 5694 10582 6460 426 551 10204 5930 0 0 2309 1579 182 151 100 100 100 100 15487 16134 1.72 .581 .581 .562 .592 1.375 52 358 .567 .95 90 2590 16420 87 96 177 186 0 6102 520 5582 .57 6333 5814 1.754 .57 -.811 -.812
7 7039 3803 458 584 6581 3219 7303 3840 727 765 6845 3256 0 0 4240 1796 680 479 85 88 78 82 9800 10101 2.044 .489 .476 .619 .476 2.582 80 448 .447 .93 100 2770 16420 87 97 195 205 0 3728 573 3156 .48 3765 3192 2.085 .466 -1.06 -1.101
8 1397 1425 348 488 1049 937 1448 1476 358 499 1100 988 0 0 300 273 89 130 100 100 98 98 1986 2088 1.12 .893 .898 .9 .904 1.391 52 303 .91 .95 80 2940 16420 88 96 213 221 0 1397 478 919 .876 1447 969 1.142 .881 -.191 -.183
9 7579 6432 322 468 7257 5964 7057 6450 327 472 6735 5982 0 0 2463 1710 43 61 100 100 100 100 13221 12717 1.217 .822 .888 .831 .893 1.421 52 377 .822 .92 90 3120 16420 87 96 230 239 0 6306 459 5847 .806 6324 5865 1.241 .871 -.312 -.2
10 1070 1055 310 459 760 596 1060 1057 320 467 750 598 0 0 194 161 50 63 100 100 100 100 1356 1348 1.275 .784 .797 .78 .776 1.29 32 229 .782 .92 70 3300 16420 88 95 249 256 0 1034 450 584 .769 1036 586 1.301 .782 -.379 -.355
11 2814 4533 310 461 2504 4072 2938 4561 312 463 2628 4100 0 0 706 723 37 50 100 100 98 100 6576 6728 .615 1.626 1.56 1.768 1.564 1.682 52 359 1.534 .95 90 3480 16430 88 97 266 275 0 4444 452 3992 1.594 4472 4020 .627 1.53 .673 .613
12 10355 5809 316 466 10039 5343 10640 6340 319 469 10324 5874 0 0 1873 1496 38 54 100 100 100 100 15382 16198 1.879 .532 .569 .506 .564 1.498 52 364 .529 .94 90 3650 16420 87 96 283 292 0 5695 457 5238 .522 6216 5759 1.916 .558 -.938 -.842
13 6209 3095 318 455 5891 2640 6273 3172 319 457 5955 2717 0 0 911 698 40 56 100 100 100 100 8531 8672 2.231 .448 .456 .431 .461 1.345 52 379 .458 .95 90 3830 16420 87 96 301 310 0 3034 446 2588 .439 3110 2664 2.276 .447 -1.187 -1.161
14 9090 5150 317 447 8773 4703 8972 5322 317 451 8655 4875 0 0 2174 1577 38 51 100 100 100 100 13476 13530 1.865 .536 .563 .509 .569 1.593 52 371 .546 .9 90 4010 16420 87 96 319 328 0 5049 438 4611 .526 5218 4779 1.903 .552 -.928 -.857
15 6715 7084 329 461 6386 6623 6656 7429 340 468 6327 6968 0 0 1608 1852 59 61 100 100 100 100 13009 13295 .964 1.037 1.101 1.009 1.103 1.464 52 388 1.074 .91 90 4180 16420 87 96 336 345 0 6945 452 6493 1.017 7283 6831 .983 1.08 .024 .111
16 5457 3742 364 493 5093 3249 5556 3925 392 501 5192 3432 0 0 1000 1031 95 84 100 100 100 100 8342 8624 1.568 .638 .661 .594 .665 1.562 52 360 .669 .93 90 4360 16420 87 96 354 363 0 3669 483 3185 .625 3848 3365 1.599 .648 -.677 -.626
17 7520 10901 387 509 7133 10392 7873 11854 412 522 7486 11345 0 0 1226 2999 98 90 100 100 100 100 17525 18831 .686 1.457 1.515 1.376 1.528 1.48 52 363 1.557 .94 90 4530 16420 87 96 371 380 0 10687 499 10188 1.428 11622 11123 .7 1.486 .514 .571
18 2570 1769 425 527 2145 1242 2150 1712 422 533 1725 1185 0 0 1159 419 87 84 100 100 100 100 3387 2910 1.727 .579 .687 .632 .641 1.658 52 319 .486 .82 80 4710 16420 88 96 390 398 0 1734 517 1218 .568 1678 1162 1.762 .673 -.817 -.57
19 7796 8776 503 597 7293 8179 7996 9306 498 593 7493 8709 0 0 1666 2129 83 81 100 100 100 100 15472 16202 .892 1.121 1.162 1.1 1.167 1.351 52 393 1.154 .94 90 4890 16420 87 96 407 416 0 8604 585 8019 1.099 9124 8538 .91 1.139 .137 .188
20 1731 8121 380 504 1351 7617 1819 7965 405 518 1439 7461 0 0 438 1682 103 90 98 100 96 100 8968 8900 .177 5.638 5.185 5.823 5.257 1.573 52 292 5.815 .93 80 5060 16430 89 97 425 433 0 7962 494 7468 5.527 7809 7315 .181 5.083 2.467 2.346

Total number of rows: 16896

Table truncated, full table size 3839 Kbytes.




Supplementary data files not provided

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