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Sample GSM132365 Query DataSets for GSM132365
Status Public on Aug 30, 2006
Title Exp. #19, Intergenic enrichment. Fixed Spheroplasts Extract (Incubted in NIB on ice o/n) vs ...
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 S288C Spheros OD 1, Fixed, Incubated in NIB 20 mins on ice, o/n ice, Beadbeat, P/C, Amplified
Organism Saccharomyces cerevisiae
Characteristics S288C Spheros OD 1, Fixed, Incubated in NIB 20 mins on ice, o/n ice, Beadbeat, P/C, Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Exp Name: Exp. #19, Intergenic enrichment. Fixed Spheroplasts Extract (Incubted in NIB on ice o/n) vs Whole Extract. Nagy 2-05-02 Crosslinks in the sample DNA were NOT REVERSED prior to Phenol Chloroform prep The reference DNA was never crosslinked. After P/C prep, samples were treated with 100 ng/uL RNAse A for 1 hour at 37 degrees.
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
1 872 1038 231 180 641 858 455 514 243 185 224 334 0 0 611 864 115 43 90 100 49 100 1499 558 .747 1.339 1.491 1.29 1.281 1.56 120 567 1.395 .96 120 1030 16620 56 68 91 103 0 763 132 631 .984 378 246 1.016 1.096 -.023 .133
2 4604 5924 225 173 4379 5751 5059 6442 245 186 4834 6269 0 0 1325 1500 128 59 98 100 96 100 10130 11103 .761 1.313 1.297 1.433 1.322 1.721 156 575 1.301 .98 140 1200 16620 55 69 107 121 0 4356 127 4229 .966 4737 4610 1.036 .954 -.05 -.069
3 7497 8098 220 161 7277 7937 8749 9530 230 173 8529 9369 0 0 2587 2948 94 69 100 100 100 100 15214 17898 .917 1.091 1.098 1.081 1.106 1.256 156 554 1.1 .98 140 1380 16610 54 68 125 139 0 5954 118 5836 .802 7007 6889 1.247 .808 -.318 -.308
4 2467 3728 220 159 2247 3569 1245 1721 614 511 1025 1562 0 0 1752 2796 1619 1451 41 50 37 45 5816 2587 .63 1.588 1.524 1.561 1.549 1.459 156 597 1.617 .96 150 1550 16610 53 68 141 156 0 2741 117 2624 1.168 1265 1149 .856 1.121 .224 .164
5 5067 6719 221 165 4846 6554 5181 6825 304 225 4960 6660 0 0 587 976 562 393 100 100 100 100 11400 11620 .739 1.352 1.343 1.345 1.35 1.153 156 556 1.357 .98 140 1720 16610 54 68 159 173 0 4940 121 4819 .994 5018 4897 1.006 .987 -.008 -.018
6 7851 6389 238 182 7613 6207 7976 6525 310 236 7738 6343 0 0 935 808 429 280 100 100 100 100 13820 14081 1.227 .815 .82 .815 .825 1.153 156 664 .801 .97 150 1900 16610 53 68 176 191 0 4698 134 4564 .599 4798 4664 1.668 .603 -.738 -.73
7 7749 8863 264 212 7485 8651 7994 8992 305 246 7730 8780 0 0 988 1073 219 172 100 100 100 100 16136 16510 .865 1.156 1.136 1.158 1.152 1.122 156 732 1.139 .98 150 2070 16610 53 68 193 208 0 6517 156 6361 .85 6612 6456 1.177 .835 -.235 -.26
8 1781 2021 304 256 1477 1765 1873 2106 323 275 1569 1850 0 0 633 600 112 107 100 100 96 100 3242 3419 .837 1.195 1.179 1.288 1.182 1.539 52 257 1.159 .95 80 2240 16600 56 64 214 222 0 1486 188 1298 .879 1549 1360 1.138 .867 -.187 -.206
9 7890 8626 264 212 7626 8414 7934 8587 288 234 7670 8375 0 0 896 1114 115 115 100 100 100 100 16040 16045 .906 1.103 1.092 1.103 1.103 1.139 156 803 1.091 .98 150 2410 16610 53 68 227 242 0 6343 156 6187 .811 6314 6158 1.233 .803 -.302 -.317
10 1820 1921 260 220 1560 1701 1846 1896 277 233 1586 1676 0 0 702 841 98 64 100 100 96 100 3261 3262 .917 1.09 1.057 1.075 1.113 1.712 32 219 1.141 .92 70 2590 16600 56 63 249 256 0 1413 162 1251 .802 1394 1232 1.247 .777 -.319 -.364
11 2573 3573 231 174 2342 3399 2658 3573 241 188 2427 3399 0 0 520 572 66 54 100 100 100 100 5741 5826 .689 1.451 1.4 1.48 1.429 1.224 156 688 1.414 .97 150 2760 16610 53 68 262 277 0 2627 128 2499 1.067 2627 2499 .937 1.03 .094 .042
12 7231 15283 223 163 7008 15120 7387 15137 228 173 7164 14974 0 0 819 2608 88 96 100 100 100 100 22128 22138 .463 2.158 2.09 2.137 2.101 1.168 156 530 2.185 .97 140 2930 16610 54 68 280 294 0 11238 120 11118 1.586 11130 11010 .63 1.537 .666 .62
13 7145 5674 221 161 6924 5513 7326 5855 225 169 7105 5694 0 0 951 802 61 78 100 100 100 100 12437 12799 1.256 .796 .801 .794 .8 1.175 156 584 .781 .97 150 3100 16610 53 68 296 311 0 4172 118 4054 .585 4305 4187 1.708 .589 -.772 -.763
14 9117 6875 222 160 8895 6715 9805 7264 226 165 9583 7104 0 0 2369 1474 39 33 100 100 100 100 15610 16687 1.325 .755 .741 .815 .749 1.676 156 494 .727 .97 140 3280 16620 55 69 315 329 0 5055 118 4938 .555 5341 5224 1.802 .545 -.849 -.875
15 3798 4745 222 163 3576 4582 4242 5205 243 191 4020 5042 0 0 2033 2470 86 95 96 99 94 99 8158 9062 .78 1.281 1.254 1.436 1.273 1.924 156 600 1.262 .97 140 3440 16620 55 69 331 345 0 3489 120 3369 .942 3827 3707 1.061 .922 -.086 -.117
16 2823 3724 219 160 2604 3564 3103 4067 230 175 2884 3907 0 0 928 1208 96 84 98 100 96 100 6168 6791 .731 1.369 1.355 1.439 1.372 1.449 156 549 1.358 .97 140 3640 16610 54 68 351 365 0 2738 118 2621 1.006 2990 2873 .994 .996 .009 -.006
17 4201 6429 220 160 3981 6269 4508 6738 226 169 4288 6578 0 0 984 1250 88 89 100 100 100 100 10250 10866 .635 1.575 1.534 1.634 1.577 1.373 156 503 1.546 .98 140 3800 16610 54 68 367 381 0 4727 118 4610 1.158 4954 4837 .864 1.128 .211 .174
18 3593 3584 219 160 3374 3424 2222 2536 223 168 2003 2376 0 0 2754 2752 78 79 100 100 98 100 6798 4379 .985 1.015 1.186 1.044 1.001 1.486 156 643 .998 .97 150 3970 16610 53 68 383 398 0 2635 118 2518 .746 1865 1747 1.34 .872 -.422 -.197
19 3895 5659 221 165 3674 5494 4113 5655 225 172 3892 5490 0 0 2291 3335 74 107 100 100 100 100 9168 9382 .669 1.495 1.411 1.518 1.474 1.351 156 541 1.493 .98 140 4150 16610 54 68 402 416 0 4161 121 4040 1.1 4158 4037 .909 1.037 .137 .053
20 1439 3823 224 168 1215 3655 828 1990 229 178 604 1822 0 0 946 2648 78 113 99 100 97 100 4870 2426 .332 3.008 3.017 3.189 3.119 1.382 156 489 2.958 .97 140 4330 16610 54 68 420 434 0 2811 124 2688 2.212 1463 1340 .452 2.218 1.145 1.149

Total number of rows: 16896

Table truncated, full table size 3906 Kbytes.




Supplementary data files not provided

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