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Sample GSM132353 Query DataSets for GSM132353
Status Public on Aug 30, 2006
Title Exp. #04, Neutral. Whole Extract vs 50 ng S288C Genomic DNA JDL 2-28-02
Sample type genomic
 
Channel 1
Source name Original S288C DNA (Derisi), 50 ng, Amplified
Organism Saccharomyces cerevisiae
Characteristics Original S288C DNA (Derisi), 50 ng, Amplified
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Whole S288C yeast OD .75, No Fix, Beadbeat, P/C, Amplified
Organism Saccharomyces cerevisiae
Characteristics Whole S288C yeast OD .75, No Fix, Beadbeat, P/C, Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description The sample DNA was never crosslinked. 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 GPL4182
Series (2)
GSE5651 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- Neutral 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 1154 1811 178 136 976 1675 1006 1471 184 145 828 1335 0 0 596 849 38 37 94 100 90 100 2651 2163 .583 1.716 1.612 2.021 1.654 2.635 52 313 1.578 .79 90 2110 17470 72 81 119 128 0 1404 105 1298 1.33 1140 1035 .752 1.25 .412 .322
2 5636 8406 190 142 5446 8264 6549 9172 226 175 6359 9030 0 0 2495 2885 151 80 90 100 88 100 13710 15389 .659 1.517 1.42 1.464 1.435 3.149 80 397 1.562 .8 100 2280 17470 72 82 136 146 0 6516 110 6406 1.176 7110 7000 .85 1.101 .234 .139
3 7826 12018 199 151 7627 11867 9740 13486 240 187 9541 13335 0 0 3689 3390 98 85 91 100 90 100 19494 22876 .643 1.556 1.398 1.604 1.37 2.58 80 407 1.511 .82 100 2460 17470 72 82 154 164 0 9316 117 9199 1.206 10454 10337 .829 1.083 .27 .116
4 7255 5776 221 166 7034 5610 7636 6153 268 190 7415 5987 0 0 1546 1499 182 84 100 100 100 100 12644 13402 1.254 .798 .807 .78 .81 1.793 80 433 .794 .86 110 2640 17470 71 82 171 182 0 4478 129 4349 .618 4770 4641 1.617 .626 -.694 -.676
5 5348 11126 196 146 5152 10980 6416 11974 215 168 6220 11828 0 0 2510 2637 74 86 92 100 88 100 16132 18048 .469 2.131 1.902 2.457 1.863 2.436 80 408 2.048 .84 100 2810 17460 71 81 189 199 0 8625 113 8512 1.652 9282 9169 .605 1.474 .724 .56
6 11542 5500 214 159 11328 5341 12650 5431 241 171 12436 5272 0 0 3906 733 87 55 100 100 92 100 16669 17708 2.121 .471 .424 .63 .424 3.755 52 329 .338 .76 90 2990 17460 71 80 207 216 0 4264 123 4140 .365 4210 4087 2.736 .329 -1.452 -1.605
7 5717 11216 205 156 5512 11060 7968 14169 229 178 7763 14013 0 0 3677 5905 77 72 87 100 80 100 16572 21776 .498 2.007 1.805 2.629 1.91 3.8 80 383 2.098 .82 100 3160 17460 71 81 224 234 0 8695 121 8574 1.555 10984 10863 .643 1.399 .637 .485
8 1506 2043 188 141 1318 1902 1074 1459 194 145 886 1318 0 0 1059 1474 52 28 91 100 91 100 3220 2204 .693 1.443 1.488 1.298 1.278 2.288 80 362 1.474 .89 100 3330 17470 72 82 241 251 0 1584 109 1474 1.119 1131 1022 .894 1.153 .162 .206
9 10692 15446 184 139 10508 15307 11685 16237 189 145 11501 16098 0 0 3481 4975 35 32 98 100 97 100 25815 27599 .686 1.457 1.4 1.286 1.407 2.392 80 427 1.667 .8 110 3510 17470 71 82 258 269 0 11974 108 11866 1.129 12587 12479 .886 1.085 .175 .118
10 1041 1114 193 151 848 963 899 896 202 156 706 745 0 0 608 592 46 38 88 100 87 100 1811 1451 .881 1.136 1.055 1.224 1.155 2.747 80 366 1.086 .83 100 3690 17470 72 82 277 287 0 864 117 747 .88 695 578 1.136 .818 -.184 -.29
11 3550 3884 221 169 3329 3715 3782 4134 275 188 3561 3965 0 0 1307 1414 181 74 93 100 92 98 7044 7526 .896 1.116 1.113 1.108 1.083 3.346 80 396 1.182 .78 110 3860 17470 71 82 293 304 0 3011 131 2880 .865 3205 3074 1.156 .863 -.209 -.212
12 10685 4959 202 154 10483 4805 11273 5362 262 174 11071 5208 0 0 2653 1581 188 77 100 100 100 100 15288 16279 2.182 .458 .47 .424 .472 2.28 80 444 .408 .82 110 4030 17470 71 82 310 321 0 3844 119 3725 .355 4157 4037 2.814 .365 -1.493 -1.455
13 5432 11101 198 151 5234 10950 5837 12063 201 153 5639 11912 0 0 1482 2719 31 31 100 100 98 100 16184 17551 .478 2.092 2.112 2.088 2.121 2.123 52 330 2.415 .79 90 4210 17470 72 81 329 338 0 8605 117 8488 1.622 9351 9234 .617 1.638 .698 .712
14 7785 9834 203 160 7582 9674 9358 11995 215 177 9155 11835 0 0 3371 4238 60 62 98 100 96 100 17256 20990 .784 1.276 1.293 1.362 1.342 4.023 80 390 1.332 .81 100 4380 17470 72 82 346 356 0 7623 124 7499 .989 9298 9174 1.011 1.002 -.016 .003
15 5231 10692 211 180 5020 10512 6316 12699 223 196 6105 12519 0 0 2261 3963 62 69 91 100 91 100 15532 18624 .478 2.094 2.051 2.033 2.071 2.527 80 414 2.208 .85 100 4560 17460 71 81 364 374 0 8288 140 8149 1.623 9844 9705 .616 1.59 .699 .669
16 3282 6080 210 182 3072 5898 3879 7715 213 187 3669 7533 0 0 1278 3131 36 50 98 98 98 98 8970 11202 .521 1.92 2.053 1.487 2.033 3.454 80 387 2.359 .81 100 4730 17470 72 82 381 391 0 4713 141 4572 1.488 5981 5840 .672 1.592 .574 .67
17 3725 7251 213 181 3512 7070 4453 8453 220 188 4240 8272 0 0 1682 3078 45 46 97 100 93 100 10582 12512 .497 2.013 1.951 1.899 1.986 3.575 80 382 2.3 .78 100 4910 17470 72 82 399 409 0 5621 140 5481 1.561 6553 6412 .641 1.512 .642 .597
18 4261 6320 210 168 4051 6152 4771 6390 220 177 4561 6222 0 0 1581 1009 49 49 100 100 98 100 10203 10783 .658 1.519 1.364 1.786 1.334 2.399 52 349 1.413 .75 90 5080 17460 71 80 416 425 0 4899 130 4769 1.177 4953 4823 .849 1.057 .235 .081
19 5888 7955 214 168 5674 7787 7004 8158 222 172 6790 7990 0 0 2250 795 59 35 100 100 96 100 13461 14780 .729 1.372 1.177 1.919 1.2 3.437 52 351 1.225 .8 90 5260 17460 71 80 434 443 0 6167 130 6036 1.064 6324 6194 .94 .912 .089 -.133
20 3091 2402 201 165 2890 2237 3718 2971 209 177 3517 2806 0 0 1354 1224 60 52 96 98 93 92 5127 6323 1.292 .774 .798 .718 .787 4.481 80 385 .761 .79 100 5440 17470 72 82 452 462 0 1862 128 1734 .6 2303 2175 1.667 .618 -.737 -.693

Total number of rows: 16896

Table truncated, full table size 3888 Kbytes.




Supplementary data files not provided

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