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Sample GSM132374 Query DataSets for GSM132374
Status Public on Aug 30, 2006
Title Exp. #29, ORF enr. Fixed Nuclear Extract (1% 30 min) *IP #2* REVERSED BEFORE P/C vs S288C Genomic
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 IP-enriched DNA, Amplified
Organism Saccharomyces cerevisiae
Characteristics IP-enriched DNA, Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description Full Name: Exp. #29, ORF enr. Fixed Nuclear Extract (1% 30 min) *IP #2* REVERSED BEFORE P/C vs S288C Genomic DNA The crosslinks in the IP-DNA were reversed prior to Phenol Chloroform prep. The S288C reference DNA (Green Channel)was sonicated, but was never subjected to crosslinking or reversal conditions. DNA was derived from the large Derisi Prep. *THESE RESULTS DO NOT REFLECT THE SPECIFICITY OF THE ANTI-H3 ANTIBODY.*.
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 GPL4184
Series (2)
GSE5649 Genomewide demarcation of RNA PolII transcription units by physical fractionation of chromatin- ORF 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 1269 1487 120 168 1149 1319 1254 1503 127 176 1134 1335 0 0 414 402 44 56 98 99 98 98 2468 2469 .871 1.148 1.177 1.179 1.153 1.146 156 744 1.113 .99 140 2110 16810 106 120 161 175 0 1005 114 891 .776 1016 902 1.289 .795 -.367 -.33
2 4162 6836 128 175 4034 6661 4246 7061 141 194 4118 6886 0 0 496 945 87 95 100 100 100 100 10695 11004 .606 1.651 1.672 1.645 1.666 1.075 156 524 1.649 .99 140 2280 16810 106 120 178 192 0 4619 118 4501 1.116 4771 4653 .896 1.13 .158 .176
3 6523 18001 127 174 6396 17827 6547 17912 145 204 6420 17738 0 0 790 2020 97 127 100 100 100 100 24223 24158 .359 2.787 2.763 2.793 2.78 1.059 156 704 2.772 1 150 2460 16800 104 119 195 210 0 12163 118 12045 1.883 12103 11985 .531 1.867 .913 .901
4 1208 3121 136 183 1072 2938 145 218 181 255 9 35 0 0 4103 10210 142 195 15 30 9 23 4010 44 .365 2.741 3.889 2.146 1.831 2.638 52 204 2.595 .95 80 2640 16740 102 110 217 225 -100 2109 124 1985 1.852 147 24 .54 2.628 .889 1.394
5 4825 8020 126 178 4699 7842 4953 8271 147 205 4827 8093 0 0 652 942 98 115 100 100 100 100 12541 12920 .599 1.669 1.677 1.677 1.669 1.068 156 734 1.656 1 150 2810 16790 103 118 230 245 0 5419 120 5299 1.128 5589 5468 .887 1.133 .173 .18
6 137 186 132 178 5 8 131 183 139 189 -1 5 0 0 27 29 46 47 6 5 2 1 13 4 .625 1.6 1.298 1.352 3.467 80 329 1.96 .55 100 2970 16790 106 116 249 259 -100 126 120 5 1.081 124 3 .925 .112
7 6118 12166 135 182 5983 11984 6331 12766 143 194 6196 12584 0 0 928 1917 57 56 100 100 100 100 17967 18780 .499 2.003 2.031 2.001 2.025 1.086 156 597 1.999 .99 140 3150 16790 104 118 265 279 0 8220 123 8097 1.353 8626 8503 .739 1.372 .437 .457
8 1303 2518 133 176 1170 2342 1264 2358 139 190 1131 2182 0 0 477 1333 42 96 100 100 100 100 3512 3313 .5 2.002 1.929 1.95 1.87 1.338 120 489 2.376 .88 130 3320 16780 103 116 282 295 0 1701 119 1582 1.353 1593 1474 .739 1.304 .436 .382
9 4931 11891 126 167 4805 11724 4972 11995 131 176 4846 11828 0 0 517 1117 30 85 100 100 100 100 16529 16674 .41 2.44 2.441 2.445 2.445 1.053 156 634 2.411 .99 150 3500 16780 102 117 299 314 0 8034 113 7922 1.649 8105 7992 .607 1.649 .721 .722
10 781 1297 124 160 657 1137 782 1285 126 162 658 1125 0 0 154 264 20 22 100 100 100 100 1794 1783 .578 1.731 1.71 1.731 1.723 1.118 120 470 1.733 .99 130 3660 16780 103 116 316 329 0 876 108 768 1.169 868 760 .855 1.155 .226 .208
11 2224 5420 125 161 2099 5259 2352 5758 127 164 2227 5597 0 0 469 1179 17 26 100 100 100 100 7358 7824 .399 2.505 2.513 2.521 2.532 1.12 156 561 2.508 .99 140 3840 16780 103 117 334 348 0 3662 109 3553 1.693 3891 3782 .591 1.698 .759 .764
12 7016 10284 128 162 6888 10122 7117 10463 130 164 6989 10301 0 0 651 958 18 28 100 100 100 100 17010 17290 .68 1.47 1.474 1.47 1.465 1.05 120 470 1.447 1 130 4010 16770 102 115 351 364 0 6949 109 6839 .993 7070 6960 1.007 .996 -.01 -.006
13 3448 10609 130 162 3318 10447 3707 11465 132 162 3577 11303 0 0 772 2304 16 16 100 100 100 100 13765 14880 .318 3.149 3.16 3.195 3.167 1.22 156 571 3.142 .99 140 4180 16770 102 116 368 382 0 7168 109 7059 2.127 7747 7637 .47 2.135 1.089 1.094
14 4292 15831 137 164 4155 15667 4391 16457 138 165 4254 16293 0 0 680 2551 15 16 100 100 100 100 19822 20547 .265 3.771 3.83 3.782 3.801 1.112 120 503 3.772 .99 130 4360 16770 102 115 386 399 0 10697 111 10586 2.548 11120 11009 .393 2.588 1.349 1.372
15 3881 8675 137 165 3744 8510 3973 8596 137 166 3836 8431 0 0 704 1609 16 18 100 100 100 100 12254 12267 .44 2.273 2.198 2.277 2.276 1.098 120 547 2.267 .99 130 4530 16760 101 114 403 416 0 5861 111 5750 1.536 5808 5697 .651 1.485 .619 .571
16 2827 5525 134 163 2693 5362 2935 5693 135 164 2801 5530 0 0 350 632 26 21 100 100 100 100 8055 8331 .502 1.991 1.974 1.998 2 1.098 120 518 1.975 .99 130 4700 16760 101 114 420 433 0 3733 110 3623 1.345 3847 3736 .743 1.334 .428 .416
17 3823 4407 125 159 3698 4248 4227 4814 127 163 4102 4655 0 0 1174 1228 27 48 99 100 98 99 7946 8757 .871 1.149 1.135 1.201 1.153 1.351 156 591 1.132 .99 140 4880 16750 100 114 438 452 0 2978 107 2870 .776 3253 3145 1.288 .767 -.366 -.383
18 3689 10067 125 157 3564 9910 3933 10596 126 162 3808 10439 0 0 897 1980 18 49 100 100 99 100 13474 14247 .36 2.781 2.741 2.929 2.74 1.419 120 549 2.713 .99 130 5050 16740 99 112 455 468 0 6802 106 6696 1.879 7159 7053 .532 1.852 .91 .889
19 4014 7366 127 159 3887 7207 4151 7490 128 160 4024 7331 0 0 780 1543 16 17 100 100 100 100 11094 11355 .539 1.854 1.822 1.86 1.891 1.153 120 564 1.867 .99 130 5230 16750 100 113 473 486 0 4977 107 4870 1.253 5061 4953 .798 1.231 .325 .3
20 2292 1869 128 160 2164 1709 2443 1991 128 161 2315 1831 0 0 527 370 16 16 100 100 100 100 3873 4146 1.266 .79 .791 .816 .79 1.3 120 566 .782 .99 130 5400 16740 99 112 490 503 0 1263 108 1155 .534 1345 1237 1.874 .534 -.906 -.904

Total number of rows: 16512

Table truncated, full table size 3787 Kbytes.




Supplementary data files not provided
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