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Sample GSM132372 Query DataSets for GSM132372
Status Public on Aug 30, 2006
Title Exp. #26, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #3* REVERSED BEFORE P/C vs Fixed Nuclea
Sample type genomic
 
Channel 1
Source name DNA prepared from IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep.
Organism Saccharomyces cerevisiae
Characteristics DNA prepared from IP Input, Amplified NOTE: NOT REVERSED prior to P/C Prep.
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.
Organism Saccharomyces cerevisiae
Characteristics "IP" DNA, Amplified THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTIBODY.
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #26, ORF+Int enr. Fixed Nuclear Extract (1% 30 min) *IP #3* REVERSED BEFORE P/C vs Fixed Nuclear Extract (1% 30 min) 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. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*
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
1 854 825 111 56 743 769 808 826 112 58 697 770 0 0 282 280 15 14 100 100 100 100 1512 1467 .966 1.035 1.105 1.031 1.044 1.218 156 764 1.03 .97 150 1820 17390 85 100 151 166 0 764 52 712 .958 765 713 1.043 1.023 -.061 .033
2 3395 4876 113 58 3282 4818 3620 5102 116 63 3507 5044 0 0 704 1202 38 35 100 100 100 100 8100 8551 .681 1.468 1.438 1.45 1.447 1.175 156 558 1.528 .97 150 1980 17380 84 99 167 182 0 4515 54 4461 1.359 4724 4670 .736 1.332 .443 .413
3 5258 12192 111 57 5147 12135 5661 12655 113 61 5550 12598 0 0 1186 1909 15 26 100 100 100 100 17282 18148 .424 2.358 2.27 2.444 2.311 1.337 156 542 2.363 .97 140 2160 17380 85 99 186 200 0 11289 53 11236 2.183 11718 11665 .458 2.102 1.126 1.072
4 125 82 109 57 16 25 119 67 109 60 10 10 0 0 31 39 14 25 40 25 18 16 41 20 .64 1.563 1 .995 .868 3.707 80 344 1.524 .62 100 2320 17370 86 96 204 214 -100 76 53 23 1.447 62 9 .691 .926 .533 -.111
5 2990 5992 106 57 2884 5935 3155 6253 107 60 3049 6196 0 0 543 1027 14 20 100 100 100 100 8819 9245 .486 2.058 2.032 2.08 2.041 1.213 156 651 2.091 .97 150 2510 17380 84 99 220 235 0 5548 53 5495 1.905 5790 5737 .525 1.882 .93 .912
6 116 59 111 59 5 0 115 58 111 60 4 -1 0 0 13 9 15 11 22 7 3 2 5 3 .77 .75 3.317 80 314 .195 .16 100 2670 17370 86 96 239 249 -100 55 55 0 54
7 4662 9292 110 60 4552 9232 4895 9949 111 64 4785 9889 0 0 877 1998 14 52 100 100 100 100 13784 14674 .493 2.028 2.067 2.006 2.056 1.309 156 611 2.087 .97 150 2840 17380 84 99 253 268 0 8604 56 8548 1.878 9212 9156 .533 1.914 .909 .936
8 1434 2239 110 62 1324 2177 1425 2046 114 71 1315 1984 0 0 644 1139 30 77 100 100 100 100 3501 3299 .608 1.644 1.509 1.639 1.587 1.408 120 442 1.731 .93 120 3010 17370 85 97 272 284 0 2073 57 2016 1.522 1894 1837 .657 1.397 .606 .482
9 3623 9539 107 59 3516 9480 3735 9980 109 63 3628 9921 0 0 641 1807 17 25 100 100 100 100 12996 13549 .371 2.696 2.735 2.681 2.718 1.222 156 564 2.789 .96 140 3190 17380 85 99 289 303 0 8832 55 8778 2.497 9241 9186 .401 2.532 1.32 1.34
10 773 1333 106 58 667 1275 772 1376 107 65 666 1318 0 0 183 389 14 62 100 100 100 100 1942 1984 .523 1.912 1.979 1.888 1.873 1.35 120 442 1.975 .97 130 3370 17380 85 98 307 320 0 1234 54 1181 1.77 1274 1220 .565 1.832 .824 .874
11 1813 4620 107 58 1706 4562 1916 4834 108 67 1809 4776 0 0 368 828 16 64 100 100 99 100 6268 6585 .374 2.674 2.64 2.758 2.665 1.425 156 552 2.696 .97 140 3540 17370 84 98 324 338 0 4278 54 4224 2.476 4476 4422 .404 2.445 1.308 1.29
12 4793 7656 106 56 4687 7600 5055 8205 107 61 4949 8149 0 0 1114 1643 14 36 100 100 100 100 12287 13098 .617 1.622 1.647 1.626 1.634 1.264 156 590 1.638 .97 150 3720 17370 83 98 341 356 0 7089 52 7037 1.501 7597 7545 .666 1.525 .586 .608
13 2530 6034 106 56 2424 5978 2693 6286 107 58 2587 6230 0 0 639 1503 13 17 100 100 100 100 8402 8817 .405 2.466 2.408 2.485 2.389 1.335 156 494 2.533 .96 140 3890 17380 85 99 359 373 0 5587 52 5535 2.283 5820 5769 .438 2.23 1.191 1.157
14 2659 11517 108 57 2551 11460 2808 12094 113 67 2700 12037 0 0 549 2026 36 50 100 100 100 100 14011 14737 .223 4.492 4.458 4.565 4.436 1.286 120 490 4.554 .97 130 4060 17370 84 97 376 389 0 10664 53 10611 4.16 11198 11145 .24 4.128 2.056 2.045
15 2944 6395 110 57 2834 6338 3224 6551 128 81 3114 6494 0 0 774 1190 151 147 100 100 99 100 9172 9608 .447 2.236 2.085 2.355 2.193 1.449 120 561 2.184 .96 130 4230 17360 83 96 393 406 0 5921 53 5869 2.071 6066 6013 .483 1.931 1.05 .949
16 2201 4242 112 58 2089 4184 2389 4424 144 93 2277 4366 0 0 572 784 212 207 99 100 95 100 6273 6643 .499 2.003 1.917 2.117 1.962 1.437 120 529 1.961 .97 130 4410 17360 83 96 411 424 0 3928 54 3874 1.855 4096 4043 .539 1.775 .891 .828
17 2209 3912 109 57 2100 3855 2467 4222 128 77 2358 4165 0 0 728 994 152 152 96 100 95 100 5955 6523 .545 1.836 1.766 2.024 1.774 1.695 156 521 1.797 .96 140 4590 17370 84 98 429 443 0 3622 53 3569 1.7 3909 3856 .588 1.635 .765 .71
18 2524 9310 111 57 2413 9253 2716 9589 112 60 2605 9532 0 0 561 1624 19 25 100 100 100 100 11666 12137 .261 3.835 3.659 3.952 3.752 1.312 120 504 3.813 .97 130 4740 17360 83 96 444 457 0 8620 53 8568 3.551 8879 8826 .282 3.388 1.828 1.76
19 2464 4998 112 56 2352 4942 2818 5574 114 58 2706 5518 0 0 825 1561 19 20 100 100 100 100 7294 8224 .476 2.101 2.039 2.184 2.043 1.683 156 613 2.136 .95 140 4940 17370 84 98 464 478 0 4628 52 4576 1.946 5161 5109 .514 1.888 .96 .917
20 7176 1507 113 58 7063 1449 7515 1549 115 58 7402 1491 0 0 1412 252 15 8 100 100 100 100 8512 8893 4.874 .205 .201 .208 .196 1.3 120 455 .193 .94 130 5120 17370 84 97 482 495 0 1395 54 1342 .19 1434 1381 5.264 .187 -2.396 -2.423

Total number of rows: 16512

Table truncated, full table size 3665 Kbytes.




Supplementary data files not provided
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