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Sample GSM132366 Query DataSets for GSM132366
Status Public on Aug 30, 2006
Title Exp. #20, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min), used as ref in jdl_g_111E vs ...
Sample type genomic
 
Channel 1
Source name Sonicated s288C Genomic DNA, Freshly Amplified
Organism Saccharomyces cerevisiae
Characteristics Sonicated s288C Genomic DNA, Freshly Amplified
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Input for Histone H3 WT IP #2 see note
Organism Saccharomyces cerevisiae
Characteristics Input for Histone H3 WT IP #2 see note
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #20, Intergenic enrichment. Fixed Nuclear Extract (1% 30 min), used as ref in jdl_g_111E vs S288C Genomic DNA Input (RED CHANNEL) was DNA from nuclei that had been salt extracted. Crosslinks in the INPUT DNA were NOT REVERSED prior to Phenol Chloroform prep. The S288C reference DNA was sonicated, but was never subjected to crosslinking or reversal conditions.
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 1112 685 208 146 904 539 538 327 210 147 330 181 0 0 1135 641 26 19 100 100 100 100 1443 511 1.677 .596 .548 .593 .579 1.606 120 578 .566 .97 120 1830 17930 69 81 126 138 0 965 206 759 .84 461 255 1.191 .773 -.252 -.372
2 7729 4272 213 150 7516 4122 8076 4396 218 154 7863 4246 0 0 1748 1161 54 35 100 100 100 100 11638 12109 1.823 .548 .54 .533 .545 1.341 156 624 .549 .97 150 2010 17930 67 82 142 157 0 6017 211 5806 .772 6192 5980 1.295 .761 -.373 -.395
3 12455 6357 214 150 12241 6207 13409 6655 220 161 13195 6505 0 0 3975 1809 38 138 100 100 100 100 18448 19700 1.972 .507 .493 .534 .507 1.511 156 553 .484 .96 140 2180 17920 67 81 160 174 0 8954 211 8742 .714 9373 9162 1.4 .694 -.486 -.526
4 6791 3176 221 156 6570 3020 7134 3342 339 235 6913 3186 0 0 1314 598 907 539 100 100 100 98 9590 10099 2.175 .46 .461 .459 .461 1.297 120 518 .441 .96 130 2350 17920 67 80 177 190 0 4473 220 4254 .647 4707 4487 1.545 .649 -.627 -.623
5 9842 4443 224 156 9618 4287 10322 4700 254 182 10098 4544 0 0 2095 872 293 221 100 100 99 100 13905 14642 2.244 .446 .45 .451 .448 1.431 156 617 .429 .96 140 2530 17920 67 81 195 209 0 6258 220 6038 .628 6620 6400 1.593 .634 -.672 -.658
6 15605 4092 227 157 15378 3935 16149 4299 231 163 15922 4142 0 0 2884 901 33 30 100 100 100 100 19313 20064 3.908 .256 .26 .25 .26 1.416 156 556 .244 .95 140 2700 17920 67 81 212 226 0 5763 221 5542 .36 6055 5834 2.775 .366 -1.472 -1.449
7 12704 7242 229 156 12475 7086 13584 7745 233 162 13355 7589 0 0 2719 1817 33 26 100 100 100 100 19561 20944 1.761 .568 .568 .557 .574 1.411 156 630 .559 .96 140 2870 17920 67 81 229 243 0 10200 220 9980 .8 10908 10689 1.25 .8 -.322 -.321
8 2227 1393 232 164 1995 1229 2025 1248 245 168 1793 1084 0 0 1195 757 62 28 100 100 100 100 3224 2877 1.623 .616 .605 .599 .599 1.658 52 228 .604 .93 80 3050 17920 70 78 250 258 0 1962 231 1731 .868 1758 1527 1.153 .852 -.205 -.232
9 12773 5718 225 157 12548 5561 13861 6181 234 163 13636 6024 0 0 3726 1685 53 33 100 100 99 100 18109 19660 2.256 .443 .442 .465 .445 1.527 208 908 .436 .97 160 3210 17920 66 82 262 278 0 8054 221 7832 .624 8706 8485 1.602 .622 -.68 -.685
10 1561 959 253 179 1308 780 1561 1021 261 181 1308 842 0 0 330 220 46 32 100 100 100 100 2088 2150 1.677 .596 .644 .58 .58 1.42 32 207 .599 .94 70 3390 17920 70 77 284 291 0 1351 252 1099 .84 1438 1186 1.191 .907 -.252 -.141
11 4782 2680 229 160 4553 2520 5105 2844 377 355 4876 2684 0 0 1209 675 2379 2233 92 80 58 0 7073 7560 1.807 .553 .55 .554 .554 1.329 156 649 .544 .96 140 3560 17920 67 81 298 312 0 3775 225 3549 .78 4006 3780 1.283 .775 -.359 -.367
12 14176 6583 227 159 13949 6424 14800 6719 385 370 14573 6560 0 0 2685 1863 2507 2353 99 94 99 85 20373 21133 2.171 .461 .45 .441 .456 1.361 156 584 .452 .95 150 3730 17920 66 81 314 329 0 9272 224 9048 .649 9463 9239 1.542 .634 -.625 -.657
13 7801 5564 232 168 7569 5396 8456 5745 237 173 8224 5577 0 0 2408 1635 33 28 100 100 100 100 12965 13801 1.403 .713 .678 .735 .696 1.756 156 516 .688 .94 140 3900 17920 67 81 332 346 0 7837 237 7600 1.004 8092 7855 .996 .955 .006 -.066
14 11760 6042 237 171 11523 5871 12509 6494 238 175 12272 6323 0 0 4189 1939 30 27 100 100 100 100 17394 18595 1.963 .51 .515 .524 .503 1.736 156 566 .483 .95 140 4070 17920 67 81 349 363 0 8510 241 8269 .718 9146 8906 1.394 .726 -.479 -.463
15 8586 6104 229 167 8357 5937 9609 6476 231 170 9380 6309 0 0 3048 1615 28 24 100 100 100 100 14294 15689 1.408 .71 .673 .809 .683 1.953 156 598 .665 .95 140 4250 17910 66 80 367 381 0 8597 235 8362 1.001 9121 8886 .999 .947 .001 -.078
16 5440 3578 217 160 5223 3418 6005 3800 220 168 5788 3640 0 0 1583 734 34 80 100 100 99 100 8641 9428 1.528 .654 .629 .719 .645 1.957 156 560 .609 .94 140 4420 17910 66 80 384 398 0 5039 225 4814 .922 5352 5127 1.085 .886 -.118 -.175
17 6710 4050 202 151 6508 3899 7521 4502 208 164 7319 4351 0 0 1942 1164 40 94 100 100 100 100 10407 11670 1.669 .599 .594 .597 .597 1.566 120 415 .583 .95 120 4600 17920 68 80 403 415 0 5704 213 5492 .844 6341 6128 1.185 .837 -.245 -.256
18 6870 3407 214 159 6656 3248 6588 3184 216 161 6374 3025 0 0 1840 967 35 24 100 100 100 100 9904 9399 2.049 .488 .475 .496 .476 1.558 120 504 .469 .94 130 4770 17910 66 79 419 432 0 4799 224 4575 .687 4485 4261 1.455 .668 -.541 -.581
19 8234 4432 222 164 8012 4268 9429 4867 225 170 9207 4703 0 0 3269 1486 33 33 100 100 100 100 12280 13910 1.877 .533 .511 .597 .523 2.028 156 599 .504 .96 140 4940 17910 66 80 436 450 0 6242 231 6011 .75 6855 6624 1.333 .719 -.414 -.475
20 3781 11788 221 165 3560 11623 3615 11734 227 174 3394 11569 0 0 1121 2693 36 40 99 100 99 100 15183 14963 .306 3.265 3.409 3.301 3.232 1.544 120 501 3.311 .95 130 5120 17910 66 79 454 467 0 16603 232 16370 4.598 16527 16294 .217 4.801 2.201 2.263

Total number of rows: 16896

Table truncated, full table size 3898 Kbytes.




Supplementary data files not provided
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