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Sample GSM132356 Query DataSets for GSM132356
Status Public on Aug 30, 2006
Title Exp. #07, Neutral. Whole Extract FIXED AFTER P/C Prep vs Whole Extract, Nagy 2-05-02
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 S288C yeast OD 1, No Fix, CSH prep (P/C), THEN FIXED, Amplified
Organism Saccharomyces cerevisiae
Characteristics S288C yeast OD 1, No Fix, CSH prep (P/C), THEN FIXED, Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description The sample DNA was not crosslinked until after the P/C Prep. The crosslinkes were not reversed prior to labeling. 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. Extract: Whole Unfixed, P/C, THEN FIXED vs Whole, Unfixed. Nagy 2-05-02
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 GPL4183
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 3125 4784 724 983 2401 3801 3510 5215 729 1001 2786 4232 0 0 1113 1343 138 159 96 100 86 100 6202 7018 .632 1.583 1.519 1.741 1.591 2.901 52 320 1.637 .76 80 930 16930 62 70 63 71 0 4089 840 3249 1.353 4457 3617 .739 1.298 .436 .377
2 5637 8790 639 922 4998 7868 6002 9412 677 946 5363 8490 0 0 1436 2245 238 305 98 100 98 99 12866 13853 .635 1.574 1.583 1.571 1.571 1.944 156 681 1.635 .9 140 1120 16960 62 76 79 93 0 7513 788 6725 1.345 8044 7256 .743 1.353 .428 .436
3 7848 12091 611 924 7237 11167 8769 13232 677 988 8158 12308 0 0 2672 3706 248 308 98 100 95 100 18404 20466 .648 1.543 1.509 1.645 1.541 2.382 120 410 1.588 .88 120 1300 16970 64 76 98 110 0 10334 790 9544 1.319 11309 10520 .758 1.289 .399 .367
4 4846 7165 639 1001 4207 6164 5313 7538 679 1051 4674 6537 0 0 1566 2369 230 471 99 95 95 94 10371 11211 .683 1.465 1.399 1.413 1.404 2.163 120 508 1.561 .85 120 1470 16940 61 73 115 127 0 6124 856 5268 1.252 6443 5587 .799 1.195 .325 .257
5 6281 9090 603 911 5678 8179 6543 9252 610 980 5940 8341 0 0 1273 1828 139 513 100 100 100 100 13857 14281 .694 1.44 1.404 1.466 1.48 1.55 120 554 1.56 .89 130 1640 16960 62 75 131 144 0 7769 779 6991 1.231 7908 7129 .812 1.2 .3 .263
6 8571 12830 574 824 7997 12006 9139 13420 589 891 8565 12596 0 0 1977 2438 131 425 100 100 99 100 20003 21161 .666 1.501 1.471 1.572 1.465 1.727 156 687 1.54 .89 150 1830 16950 60 75 149 164 0 10966 704 10262 1.283 11470 10766 .779 1.257 .36 .33
7 9345 13738 566 798 8779 12940 9779 14131 638 865 9213 13333 0 0 1836 2155 370 423 100 100 99 100 21719 22546 .678 1.474 1.447 1.511 1.442 1.414 156 701 1.516 .9 140 2000 16950 61 75 167 181 0 11742 682 11060 1.26 12078 11396 .794 1.237 .333 .307
8 4378 7112 656 953 3722 6159 4587 7010 820 1078 3931 6057 0 0 1793 2195 619 597 90 100 90 100 9881 9988 .604 1.655 1.541 1.859 1.621 2.149 32 190 1.677 .76 70 2140 16950 64 71 184 191 0 6079 815 5264 1.414 5991 5177 .707 1.317 .5 .397
9 8332 12705 525 642 7807 12063 8884 13143 608 722 8359 12501 0 0 2080 2071 465 379 98 100 96 100 19870 20860 .647 1.545 1.496 1.572 1.509 1.477 156 879 1.54 .9 150 2350 16940 59 74 201 216 0 10859 549 10310 1.321 11233 10685 .757 1.278 .401 .354
10 2508 3896 450 559 2058 3337 2370 3400 547 602 1920 2841 0 0 748 1594 629 272 100 100 90 100 5395 4761 .617 1.621 1.48 1.564 1.482 1.458 32 176 1.57 .71 70 2490 16970 66 73 219 226 0 3330 478 2852 1.386 2906 2428 .722 1.265 .471 .339
11 3456 5177 526 705 2930 4472 3872 5408 594 713 3346 4703 0 0 1287 1514 655 336 89 98 84 95 7402 8049 .655 1.526 1.406 1.553 1.405 2.664 156 761 1.54 .83 140 2690 16940 60 74 236 250 0 4425 603 3822 1.305 4622 4020 .767 1.201 .384 .265
12 8926 12916 545 752 8381 12164 9717 13327 836 888 9172 12575 0 0 2238 1773 1359 750 98 100 95 100 20545 21747 .689 1.451 1.371 1.557 1.384 1.772 120 595 1.427 .85 130 2870 16940 60 73 254 267 0 11039 643 10397 1.24 11391 10748 .806 1.172 .311 .229
13 7885 10985 638 898 7247 10087 8478 11285 1121 1158 7840 10387 0 0 1829 1654 1617 869 96 100 93 100 17334 18227 .718 1.392 1.325 1.429 1.328 1.595 120 567 1.396 .81 130 3040 16940 60 73 271 284 0 9389 768 8621 1.19 9645 8878 .841 1.132 .251 .179
14 9219 13079 578 811 8641 12268 10431 14144 871 1001 9853 13333 0 0 3405 3565 1176 699 92 100 89 100 20909 23186 .704 1.42 1.353 1.604 1.332 2.202 156 659 1.381 .88 140 3220 16950 61 75 289 303 0 11179 693 10485 1.213 12089 11396 .824 1.157 .279 .21
15 6704 10571 545 758 6159 9813 7862 11437 707 902 7317 10679 0 0 2469 2182 635 528 97 100 91 100 15972 17996 .628 1.593 1.459 1.831 1.497 1.888 80 469 1.507 .84 110 3370 16940 61 72 305 316 0 9035 648 8387 1.362 9775 9127 .734 1.247 .445 .319
16 4288 6544 573 788 3715 5756 4454 6757 754 1028 3881 5969 0 0 1463 1964 564 659 92 98 91 96 9471 9850 .645 1.549 1.538 1.579 1.486 2.258 156 667 1.641 .81 140 3570 16950 61 75 324 338 0 5593 674 4920 1.324 5775 5102 .755 1.315 .405 .395
17 5703 8623 543 741 5160 7882 5962 8839 564 755 5419 8098 0 0 1412 1732 112 165 99 100 99 100 13042 13517 .655 1.528 1.494 1.608 1.532 1.777 120 445 1.575 .86 130 3750 16950 61 74 342 355 0 7370 633 6737 1.306 7555 6921 .766 1.277 .385 .353
18 6606 10107 589 854 6017 9253 7435 11360 603 853 6846 10506 0 0 3202 4663 160 203 98 100 95 97 15270 17352 .65 1.538 1.535 1.65 1.509 2.489 156 591 1.612 .85 140 3920 16950 61 75 359 373 0 8638 730 7909 1.314 9709 8979 .761 1.312 .394 .391
19 7104 11132 630 954 6474 10178 8276 12452 663 994 7646 11498 0 0 3523 5344 152 186 97 100 97 99 16652 19144 .636 1.572 1.504 1.684 1.56 2.812 120 436 1.647 .87 120 4070 16960 63 75 375 387 0 9515 815 8699 1.344 10643 9827 .744 1.285 .426 .362
20 4428 7240 606 894 3822 6346 4548 7763 626 964 3942 6869 0 0 2727 4337 128 546 99 100 97 90 10168 10811 .602 1.66 1.743 1.703 1.544 2.227 120 510 1.719 .89 130 4250 16950 61 74 392 405 0 6188 764 5424 1.419 6635 5871 .705 1.489 .505 .575

Total number of rows: 16896

Table truncated, full table size 3837 Kbytes.




Supplementary data files not provided

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