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Sample GSM132368 Query DataSets for GSM132368
Status Public on Aug 30, 2006
Title Exp. #22, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min, samples from jdl_g_50J and 52J...
Sample type genomic
 
Channel 1
Source name Sonicated s288C Genomic DNA, Amplified Date of Experiment
Organism Saccharomyces cerevisiae
Characteristics Sonicated s288C Genomic DNA, Amplified Date of Experiment
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Unreversed Input from WT IP #2+3 before debris clearing spin
Organism Saccharomyces cerevisiae
Characteristics Unreversed Input from WT IP #2+3 before debris clearing spin
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #22, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min, samples from jdl_g_50J and 52J) vs S288C Genomic DNA This array is the same as jdl_g_061k, except the crosslinks were not reversed. The same as jdl_g_050J and jdl_g_052J, but an independent amplification and hyb for both sample and reference. The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. S288C reference DNA was derived from the large Derisi Prep. Input was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT 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 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
1 637 1115 143 289 494 826 438 819 150 300 295 530 0 0 406 627 66 130 93 92 90 85 1320 825 .598 1.672 1.797 1.697 1.684 1.706 120 654 1.601 .95 130 1130 16770 55 68 106 119 0 764 198 566 1.145 561 363 .873 1.231 .196 .299
2 4180 6485 145 296 4035 6189 4530 7119 158 324 4385 6823 0 0 2205 3227 77 222 98 98 96 94 10224 11208 .652 1.534 1.556 1.589 1.5 1.701 156 615 1.527 .97 140 1300 16770 55 69 123 137 0 4442 203 4239 1.051 4876 4673 .952 1.066 .071 .092
3 8750 15534 159 315 8591 15219 10580 17981 170 362 10421 17666 0 0 3837 6342 67 284 100 100 99 100 23810 28087 .564 1.772 1.695 1.831 1.755 1.273 120 424 1.739 .98 120 1480 16790 58 70 142 154 0 10640 216 10424 1.213 12316 12100 .824 1.161 .279 .216
4 5651 6125 145 294 5506 5831 6396 6485 157 328 6251 6191 0 0 3092 3097 67 233 99 100 99 100 11337 12442 .944 1.059 .99 1.13 1.045 1.663 120 500 1.04 .97 120 1650 16760 55 67 159 171 0 4195 201 3994 .725 4442 4240 1.379 .678 -.463 -.56
5 7335 9824 145 295 7190 9529 7818 10361 169 331 7673 10066 0 0 1868 2047 131 219 99 100 98 100 16719 17739 .755 1.325 1.312 1.395 1.305 1.55 156 576 1.307 .97 140 1830 16780 56 70 176 190 0 6729 202 6527 .908 7097 6895 1.102 .899 -.14 -.154
6 10869 16539 159 319 10710 16220 12017 17736 230 383 11858 17417 0 0 3525 4495 536 349 97 100 97 100 26930 29275 .66 1.514 1.469 1.643 1.483 1.756 120 496 1.485 .97 120 2000 16760 55 67 194 206 0 11328 218 11110 1.037 12148 11929 .964 1.006 .053 .009
7 9909 15942 168 329 9741 15613 10364 17199 265 448 10196 16870 0 0 1977 3727 497 467 99 100 99 100 25354 27066 .624 1.603 1.655 1.578 1.627 1.476 156 704 1.651 .96 140 2180 16790 57 71 211 225 0 10919 225 10694 1.098 11780 11555 .911 1.133 .135 .18
8 1375 2583 177 330 1198 2253 1281 2464 206 395 1104 2134 0 0 622 867 111 210 96 100 93 100 3451 3238 .532 1.881 1.933 2.122 1.919 1.721 32 209 1.786 .94 70 2330 16750 56 63 229 236 0 1769 226 1543 1.288 1688 1462 .776 1.324 .365 .405
9 11222 20509 154 304 11068 20205 11374 20383 230 406 11220 20079 0 0 1970 3189 556 766 100 100 99 100 31273 31299 .548 1.826 1.79 1.853 1.815 1.261 156 818 1.85 .96 150 2530 16790 56 71 245 260 0 14047 208 13839 1.25 13961 13753 .8 1.226 .322 .294
10 792 1519 146 286 646 1233 798 1553 156 298 652 1267 0 0 210 406 45 83 100 100 100 100 1879 1919 .524 1.909 1.943 1.903 1.945 1.259 52 270 1.948 .95 80 2680 16770 58 66 264 272 0 1040 196 845 1.307 1064 868 .765 1.331 .387 .413
11 4129 6840 152 306 3977 6534 4086 6950 184 348 3934 6644 0 0 726 1222 270 289 100 100 99 100 10511 10578 .609 1.643 1.689 1.653 1.667 1.282 156 664 1.698 .95 140 2880 16800 58 72 281 295 0 4685 210 4475 1.125 4760 4551 .889 1.157 .17 .21
12 10658 20797 153 309 10505 20488 11283 21553 225 418 11130 21244 0 0 2344 3022 452 757 99 100 99 100 30993 32374 .513 1.95 1.909 2.042 1.9 1.412 156 547 1.937 .96 140 3050 16800 58 72 298 312 0 14245 212 14033 1.336 14762 14551 .749 1.307 .418 .387
13 6861 10471 152 309 6709 10162 7717 11154 185 342 7565 10845 0 0 2198 2217 224 232 96 100 96 100 16871 18410 .66 1.515 1.434 1.737 1.444 1.875 120 565 1.459 .95 130 3210 16790 57 70 314 327 0 7172 212 6960 1.037 7640 7428 .964 .982 .053 -.026
14 9678 14423 166 328 9512 14095 9973 14829 257 406 9807 14501 0 0 1578 2220 600 437 100 100 100 100 23607 24308 .675 1.482 1.479 1.49 1.489 1.206 80 470 1.507 .97 110 3400 16790 58 69 334 345 0 9879 225 9654 1.015 10157 9932 .985 1.013 .021 .018
15 5710 9134 164 322 5546 8812 5889 9263 251 398 5725 8941 0 0 1822 2429 574 422 98 100 95 100 14358 14666 .629 1.589 1.562 1.663 1.529 1.616 120 523 1.576 .95 120 3580 16790 58 70 352 364 0 6256 221 6036 1.088 6345 6124 .919 1.07 .122 .097
16 4445 6691 160 314 4285 6377 4637 6890 187 346 4477 6576 0 0 1128 1540 105 155 99 100 99 100 10662 11053 .672 1.488 1.469 1.552 1.485 1.577 156 553 1.489 .96 140 3750 16810 59 73 368 382 0 4583 215 4368 1.019 4719 4504 .981 1.006 .028 .009
17 7336 8601 142 279 7194 8322 7719 9231 160 301 7577 8952 0 0 1969 2127 55 102 99 100 99 100 15516 16529 .864 1.157 1.181 1.207 1.138 1.782 120 427 1.156 .95 120 3930 16800 59 71 387 399 0 5891 191 5700 .792 6323 6132 1.262 .809 -.336 -.305
18 7558 11085 156 317 7402 10768 9804 13399 210 358 9648 13082 0 0 4402 5677 331 276 97 100 96 100 18170 22730 .687 1.455 1.356 1.647 1.435 2.025 80 434 1.427 .95 110 4090 16790 58 69 403 414 0 7592 217 7375 .996 9177 8960 1.004 .929 -.005 -.107
19 7739 11495 158 310 7581 11185 8063 11639 310 446 7905 11329 0 0 1847 1682 741 668 100 100 97 100 18766 19234 .678 1.475 1.433 1.54 1.451 1.395 80 497 1.441 .96 110 4270 16800 59 70 421 432 0 7873 212 7661 1.011 7972 7760 .99 .982 .015 -.027
20 3978 7526 169 330 3809 7196 4856 8820 457 698 4687 8490 0 0 1616 2610 985 1294 98 100 80 92 11005 13177 .529 1.889 1.811 1.981 1.775 1.663 52 353 1.843 .94 90 4440 16800 60 69 439 448 0 5155 226 4929 1.294 6041 5815 .773 1.241 .372 .311

Total number of rows: 16896

Table truncated, full table size 3917 Kbytes.




Supplementary data files not provided
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