NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM132358 Query DataSets for GSM132358
Status Public on Aug 30, 2006
Title Exp. #09, Intergenic enrichment. Fixed Whole Extract (1% 15 min, High Phenol/Aq) vs Whole Extract
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) High Phenol/Aq, Amplified Nagy 4-25
Organism Saccharomyces cerevisiae
Characteristics Extract: Whole Fixed Yeast (1% 15 min) CSH Prep (P/C) High Phenol/Aq, Amplified Nagy 4-25
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #9, Intergenic enrichment. Fixed Whole Extract (1% 15 min, High Phenol/Aq) vs Whole Extract Nagy 4-25-02
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)
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
1 450 271 83 52 367 219 223 161 84 53 140 109 0 0 429 225 14 15 100 100 100 99 586 249 1.676 .597 .779 .674 .649 1.533 120 651 .543 .97 130 1580 17000 68 81 126 139 0 565 108 456 1.243 335 227 .804 1.622 .314 .698
2 3402 1352 82 53 3320 1299 3571 1398 83 54 3489 1345 0 0 732 349 14 16 100 100 100 100 4619 4834 2.556 .391 .385 .386 .397 1.224 156 542 .387 .98 140 1760 17000 68 82 144 158 0 2817 110 2706 .815 2913 2802 1.227 .803 -.295 -.316
3 5310 2576 81 54 5229 2522 5575 2712 82 55 5494 2658 0 0 1209 602 12 17 100 100 100 100 7751 8152 2.073 .482 .484 .489 .484 1.28 156 492 .476 .98 140 1930 17000 68 82 161 175 0 5367 113 5254 1.005 5650 5538 .995 1.008 .007 .011
4 2224 442 82 55 2142 387 1546 336 252 136 1464 281 0 0 1182 227 864 419 92 39 47 2 2529 1745 5.535 .181 .192 .178 .18 1.358 156 559 .18 .95 140 2100 17000 68 82 178 192 0 921 115 806 .376 700 585 2.657 .4 -1.41 -1.322
5 4157 1319 85 58 4072 1261 4316 1351 185 101 4231 1293 0 0 727 249 581 259 100 100 98 98 5333 5524 3.229 .31 .306 .309 .306 1.162 156 639 .305 .98 150 2280 17000 67 82 195 210 0 2748 121 2627 .645 2815 2694 1.55 .637 -.632 -.651
6 5611 1795 87 55 5524 1740 5791 1860 88 59 5704 1805 0 0 1037 363 18 40 100 100 100 100 7264 7509 3.175 .315 .316 .313 .317 1.263 156 580 .307 .98 150 2450 17000 67 82 212 227 0 3740 115 3625 .656 3875 3760 1.524 .659 -.608 -.601
7 7428 3281 87 55 7341 3226 7782 3492 91 60 7695 3437 0 0 1275 821 47 26 100 100 100 100 10567 11132 2.276 .439 .447 .417 .449 1.581 156 645 .438 .97 150 2630 17000 67 82 230 245 0 6835 115 6721 .916 7275 7160 1.092 .931 -.127 -.104
8 666 318 86 57 580 261 428 233 89 61 342 176 0 0 558 240 19 28 100 92 100 83 841 518 2.222 .45 .515 .458 .45 1.532 80 399 .429 .96 110 2810 16990 68 79 250 261 0 663 119 544 .938 485 367 1.067 1.072 -.093 .1
9 5958 4271 89 57 5869 4214 6069 4286 90 59 5980 4229 0 0 1277 1061 16 21 100 100 100 100 10083 10209 1.393 .718 .707 .71 .713 1.282 156 688 .724 .98 150 2970 17000 67 82 264 279 0 8898 119 8779 1.496 8929 8810 .669 1.473 .581 .559
10 289 189 87 54 202 135 197 150 87 56 110 96 0 0 190 114 15 18 100 95 98 87 337 206 1.496 .668 .873 .739 .771 1.864 80 349 .625 .9 100 3170 17000 70 80 287 297 0 394 113 281 1.392 313 200 .718 1.818 .477 .862
11 1792 771 84 53 1708 718 1803 804 85 54 1719 751 0 0 410 156 14 16 100 100 100 100 2426 2470 2.379 .42 .437 .421 .422 1.339 156 541 .403 .96 140 3330 16990 67 81 301 315 0 1606 110 1496 .876 1675 1565 1.142 .91 -.191 -.136
12 6799 3004 85 57 6714 2947 7042 2897 87 58 6957 2840 0 0 1126 845 23 23 100 100 100 100 9661 9797 2.278 .439 .408 .427 .439 1.303 156 546 .438 .95 150 3500 16990 66 81 317 332 0 6258 119 6140 .914 6035 5917 1.094 .85 -.129 -.234
13 5225 1155 84 54 5141 1101 5407 1206 91 59 5323 1152 0 0 1002 236 65 33 100 100 100 100 6242 6475 4.669 .214 .216 .214 .218 1.274 156 526 .208 .97 140 3670 16990 67 81 335 349 0 2406 113 2294 .446 2513 2400 2.241 .451 -1.164 -1.149
14 6531 1803 83 55 6448 1748 6809 1889 89 60 6726 1834 0 0 1789 510 62 32 100 100 99 100 8196 8560 3.689 .271 .273 .268 .271 1.368 156 547 .266 .98 140 3850 16990 67 81 353 367 0 3756 115 3642 .565 3935 3821 1.771 .568 -.824 -.816
15 3537 4928 82 53 3455 4875 3617 5027 94 61 3535 4974 0 0 615 1013 72 41 100 100 100 100 8330 8509 .709 1.411 1.407 1.409 1.419 1.264 156 623 1.423 .97 150 4020 16990 66 81 369 384 0 10267 110 10156 2.94 10473 10363 .34 2.931 1.556 1.552
16 2293 2409 82 54 2211 2355 2355 2522 92 60 2273 2468 0 0 352 472 65 36 100 100 100 100 4566 4741 .939 1.065 1.086 1.052 1.084 1.232 156 581 1.075 .98 150 4200 16990 66 81 387 402 0 5019 113 4906 2.219 5254 5142 .451 2.262 1.15 1.178
17 3991 2031 83 53 3908 1978 4215 2162 84 55 4132 2109 0 0 1024 546 13 17 100 100 100 100 5886 6241 1.976 .506 .51 .507 .511 1.339 156 529 .5 .97 140 4370 16990 67 81 405 419 0 4231 110 4121 1.054 4504 4394 .948 1.063 .077 .089
18 3008 1650 83 54 2925 1596 3019 1690 85 55 2936 1636 0 0 704 528 13 16 100 100 100 100 4521 4572 1.833 .546 .557 .516 .55 1.471 156 576 .554 .97 140 4550 16990 67 81 423 437 0 3438 113 3325 1.137 3521 3408 .88 1.161 .185 .215
19 4543 1466 82 53 4461 1413 4706 1562 84 57 4624 1509 0 0 856 378 13 22 100 100 100 100 5874 6133 3.157 .317 .326 .307 .321 1.314 156 533 .314 .97 140 4730 16990 67 81 441 455 0 3054 110 2944 .66 3254 3144 1.515 .68 -.6 -.557
20 1826 4155 83 56 1743 4099 1634 4178 86 61 1551 4122 0 0 684 964 16 30 100 100 100 100 5842 5673 .425 2.352 2.658 2.439 2.497 1.266 120 424 2.295 .95 130 4900 16990 67 80 458 471 0 8656 117 8540 4.899 8704 8588 .204 5.537 2.293 2.469

Total number of rows: 16896

Table truncated, full table size 3682 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap