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Sample GSM132373 Query DataSets for GSM132373
Status Public on Aug 30, 2006
Title Exp. #27, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *Mock IP, No Ab* REVERSED BEFORE P/C vs Fix
Sample type genomic
 
Channel 1
Source name DNA prepared from mock IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep
Organism Saccharomyces cerevisiae
Characteristics DNA prepared from mock IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Mock IP-enriched DNA, Amplified (Results not dependent on IP procedure)
Organism Saccharomyces cerevisiae
Characteristics Mock IP-enriched DNA, Amplified (Results not dependent on IP procedure)
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #27, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *Mock IP, No Ab* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) Old Name: Mock #1, No Histone H3 lysine 4 methylated Ab, wild-type vs unreversed input DNA No Antibody Mock for Anti-Histone H3 lysine 4 methylated, wild-type #1 Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep.
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 GPL4184
Series (2)
GSE5650 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- ORF-INT 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 4035 2572 284 181 3751 2391 4004 2538 290 189 3720 2357 0 0 1203 629 86 60 100 100 100 100 6142 6077 1.569 .637 .634 .651 .644 1.14 156 841 .614 .99 150 2490 15950 88 103 111 126 0 3713 261 3452 .92 3664 3403 1.087 .915 -.12 -.129
2 7952 4612 282 181 7670 4431 8227 4698 286 185 7945 4517 0 0 1530 782 39 49 100 100 100 100 12101 12462 1.731 .578 .569 .582 .582 1.096 156 519 .568 .99 140 2660 15940 88 102 129 143 0 6658 261 6397 .834 6782 6521 1.199 .821 -.262 -.285
3 15028 9665 280 178 14748 9487 15684 10198 283 181 15404 10020 0 0 2738 1722 32 29 100 100 100 100 24235 25424 1.555 .643 .65 .644 .644 1.106 156 622 .635 .99 150 2830 15940 87 102 145 160 0 13952 257 13696 .929 14722 14465 1.077 .939 -.107 -.091
4 273 184 283 179 -10 5 273 182 284 182 -10 3 0 0 28 22 33 30 3 15 0 3 -5 -7 .64 .577 3.966 80 367 .686 .33 100 3000 15920 88 98 165 175 -50 266 258 7 263 4
5 8528 5610 280 177 8248 5433 8960 5879 281 179 8680 5702 0 0 1654 1096 27 23 100 100 100 100 13681 14382 1.518 .659 .657 .658 .664 1.09 156 725 .654 .99 150 3180 15930 86 101 180 195 0 8099 256 7843 .951 8487 8231 1.052 .948 -.073 -.077
6 266 174 282 177 -16 -3 274 181 284 178 -8 4 0 0 42 24 27 22 8 12 0 0 -19 -4 .848 .844 4.399 80 373 .172 .12 100 3350 15920 88 98 200 210 -50 251 256 -4 261 6
7 13465 7403 275 176 13190 7227 14477 7805 281 186 14202 7629 0 0 3056 1470 185 119 100 100 100 100 20417 21831 1.825 .548 .537 .558 .543 1.176 156 696 .539 .99 150 3530 15930 86 101 215 230 0 10687 254 10433 .791 11267 11013 1.264 .775 -.338 -.367
8 2919 2222 274 181 2645 2041 2818 2248 265 182 2544 2067 0 0 1292 890 65 63 98 97 97 97 4686 4611 1.296 .772 .813 .792 .78 1.229 120 491 .744 .99 130 3700 15930 87 100 233 246 0 3208 261 2946 1.114 3245 2984 .898 1.173 .156 .23
9 11985 6645 275 179 11710 6466 12147 6834 277 179 11872 6655 0 0 1754 866 28 22 100 100 100 100 18176 18527 1.811 .552 .561 .556 .553 1.109 156 616 .536 .99 150 3880 15940 87 102 250 265 0 9593 258 9334 .797 9866 9607 1.255 .809 -.327 -.305
10 1919 1452 280 178 1639 1274 1997 1491 280 179 1717 1313 0 0 478 316 28 22 100 100 100 100 2913 3030 1.286 .777 .765 .794 .79 1.168 120 483 .758 .99 130 4060 15930 87 100 269 282 0 2096 257 1839 1.122 2152 1895 .891 1.104 .166 .143
11 4806 3434 277 175 4529 3259 4986 3574 276 176 4709 3399 0 0 905 602 26 22 100 100 100 100 7788 8108 1.39 .72 .722 .724 .722 1.096 156 599 .708 .99 150 4230 15930 86 101 285 300 0 4957 253 4705 1.039 5159 4907 .963 1.042 .055 .059
12 15593 7030 271 174 15322 6856 16437 7528 273 175 16166 7354 0 0 4169 1673 28 27 100 100 100 100 22178 23520 2.235 .447 .455 .455 .446 1.129 156 538 .439 .99 140 4400 15930 87 101 303 317 0 10149 251 9897 .646 10867 10616 1.548 .657 -.63 -.607
13 8298 6379 270 174 8028 6205 8493 6644 272 175 8223 6470 0 0 1083 794 28 27 100 100 100 100 14233 14693 1.294 .773 .787 .774 .776 1.055 120 482 .764 .99 130 4580 15930 87 100 321 334 0 9209 251 8958 1.116 9591 9340 .896 1.136 .158 .184
14 7604 7750 269 174 7335 7576 7861 8142 269 173 7592 7968 0 0 1728 1650 25 20 100 100 100 100 14911 15560 .968 1.033 1.05 1.039 1.039 1.095 120 466 1.021 .99 120 4750 15920 87 99 339 351 0 11188 251 10937 1.491 11754 11503 .671 1.515 .576 .599
15 8349 5954 270 173 8079 5781 8833 6423 270 173 8563 6250 0 0 1873 1420 27 22 100 100 100 100 13860 14813 1.398 .716 .73 .713 .716 1.107 120 506 .717 .99 120 4920 15920 87 99 356 368 0 8595 250 8345 1.033 9272 9023 .968 1.054 .047 .075
16 5308 3640 267 172 5041 3468 5606 3913 269 173 5339 3741 0 0 1236 859 27 23 100 100 100 100 8509 9080 1.454 .688 .701 .689 .689 1.117 120 559 .686 .99 130 5100 15920 86 99 373 386 0 5255 248 5006 .993 5649 5401 1.007 1.012 -.01 .017
17 7045 4162 268 172 6777 3990 7333 4380 269 172 7065 4208 0 0 1481 794 25 21 100 100 100 100 10767 11273 1.698 .589 .596 .604 .584 1.249 120 465 .578 .99 120 5280 15930 88 100 392 404 0 6008 248 5760 .85 6323 6075 1.177 .86 -.235 -.218
18 7984 6916 266 171 7718 6745 8403 7192 266 172 8137 7021 0 0 1639 1404 28 27 100 100 100 100 14463 15158 1.144 .874 .863 .877 .869 1.098 120 515 .865 .99 120 5450 15920 87 99 409 421 0 9984 247 9737 1.262 10382 10136 .793 1.246 .335 .317
19 5247 5119 267 171 4980 4948 6031 5209 267 172 5764 5038 0 0 2498 2271 26 23 96 100 96 100 9928 10802 1.006 .994 .874 1.107 1.004 1.588 120 517 .97 .98 120 5630 15920 87 99 427 439 0 7390 247 7143 1.434 7520 7273 .697 1.262 .52 .335
20 6299 3229 265 169 6034 3060 7204 3500 267 171 6939 3331 0 0 2840 1322 24 21 95 100 95 100 9094 10270 1.972 .507 .48 .544 .489 1.469 120 476 .49 .98 120 5810 15920 87 99 445 457 0 4661 244 4417 .732 5053 4809 1.366 .693 -.45 -.529

Total number of rows: 16512

Table truncated, full table size 3715 Kbytes.




Supplementary data files not provided

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