NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM132359 Query DataSets for GSM132359
Status Public on Aug 30, 2006
Title Exp. #11, Intergenic enrichment. Fixed Whole Extract (1% 30 min) vs Whole Extract JDL 2-28-02
Sample type genomic
 
Channel 1
Source name S288C yeast OD .75, No Fix, Beadbeat, P/C, Amplified
Organism Saccharomyces cerevisiae
Characteristics S288C yeast OD .75, No Fix, Beadbeat, P/C, Amplified
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Whole S288C yeast OD .75, Fixed, Beadbeat, P/C, Amplified
Organism Saccharomyces cerevisiae
Characteristics Whole S288C yeast OD .75, Fixed, Beadbeat, P/C, Amplified
Extracted molecule genomic DNA
Label Cy5
 
 
Description 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 GPL4184
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 2984 1901 138 127 2846 1774 3042 1958 166 148 2904 1831 0 0 1296 769 139 92 100 100 100 100 4620 4735 1.604 .623 .631 .634 .627 1.121 208 990 .613 .99 160 1850 16520 70 86 152 168 0 2347 157 2190 .77 2417 2260 1.299 .778 -.378 -.361
2 9833 7127 144 135 9689 6992 10367 7507 251 214 10223 7372 0 0 1709 1287 280 192 100 100 100 100 16681 17595 1.386 .722 .721 .723 .723 1.076 156 521 .717 1 140 2010 16510 70 84 169 183 0 8799 167 8632 .891 9268 9101 1.122 .89 -.167 -.168
3 16599 15742 140 130 16459 15612 17576 16566 206 180 17436 16436 0 0 2829 2707 240 167 100 100 100 100 32071 33872 1.054 .949 .943 .949 .951 1.051 156 645 .945 1 150 2190 16510 69 84 186 201 0 19435 160 19274 1.171 20452 20291 .854 1.164 .228 .219
4 140 122 139 129 1 -7 139 122 168 147 0 -7 0 0 18 14 211 130 0 0 0 0 -6 -7 .824 .737 4.949 80 352 .492 .89 100 2360 16510 72 82 206 216 -50 151 159 -9 151
5 13197 7396 138 126 13059 7270 13741 7721 172 145 13603 7595 0 0 1742 1095 220 120 100 100 100 100 20329 21198 1.796 .557 .558 .555 .557 1.064 156 722 .555 1 150 2540 16500 68 83 221 236 0 9131 156 8975 .687 9532 9377 1.455 .689 -.541 -.537
6 141 124 140 127 1 -3 142 124 150 134 2 -3 0 0 20 16 73 62 0 0 0 0 -2 -1 .894 .793 3.524 80 343 .072 .03 100 2700 16500 71 81 240 250 -50 153 157 -4 153
7 18083 10980 146 129 17937 10851 19145 11681 260 186 18999 11552 0 0 4302 2524 718 297 98 100 98 99 28788 30551 1.653 .605 .608 .62 .605 1.221 156 648 .598 1 140 2880 16510 70 84 256 270 0 13556 159 13396 .747 14421 14262 1.339 .751 -.421 -.414
8 6434 4292 143 134 6291 4158 6372 4059 231 207 6229 3925 0 0 2887 1930 477 363 100 100 100 100 10449 10154 1.513 .661 .63 .664 .658 1.141 120 505 .657 .98 130 3070 16510 70 83 275 288 0 5299 165 5133 .816 5011 4846 1.226 .778 -.293 -.362
9 13601 14692 138 129 13463 14563 14112 15147 174 174 13974 15018 0 0 2004 2195 236 299 100 100 100 100 28026 28992 .924 1.082 1.075 1.082 1.084 1.057 156 660 1.079 1 150 3240 16500 68 83 291 306 0 18138 159 17979 1.335 18700 18541 .749 1.327 .417 .408
10 1794 1924 139 129 1655 1795 1868 1995 147 139 1729 1866 0 0 460 462 104 82 100 100 100 100 3450 3595 .922 1.085 1.079 1.093 1.068 1.118 120 457 1.069 .99 120 3410 16500 70 82 310 322 0 2375 159 2216 1.339 2463 2304 .747 1.332 .421 .414
11 4237 3105 140 129 4097 2976 4365 3146 147 149 4225 3017 0 0 579 412 97 151 100 100 100 100 7073 7242 1.377 .726 .714 .727 .728 1.069 120 534 .719 1 130 3580 16500 69 82 326 339 0 3833 159 3674 .897 3884 3725 1.115 .882 -.157 -.182
12 4858 16122 140 129 4718 15993 5135 17096 142 150 4995 16967 0 0 925 3470 25 164 100 100 100 100 20711 21962 .295 3.39 3.397 3.371 3.409 1.085 120 556 3.396 .99 130 3750 16490 68 81 343 356 0 19904 159 19744 4.185 21106 20947 .239 4.194 2.065 2.068
13 11323 5103 140 128 11183 4975 11560 5234 143 140 11420 5106 0 0 2609 1031 24 136 100 100 100 100 16158 16526 2.248 .445 .447 .449 .442 1.086 120 532 .436 .99 130 3930 16500 69 82 361 374 0 6300 158 6142 .549 6462 6304 1.821 .552 -.865 -.857
14 12003 8182 137 127 11866 8055 13021 8489 138 127 12884 8362 0 0 2592 1490 24 21 100 100 100 100 19921 21246 1.473 .679 .649 .687 .679 1.107 120 525 .666 .99 130 4100 16500 69 82 378 391 0 10101 157 9944 .838 10480 10323 1.193 .801 -.255 -.32
15 12881 5537 137 125 12744 5412 13078 5665 137 124 12941 5540 0 0 1935 841 21 18 100 100 100 100 18156 18481 2.355 .425 .428 .425 .425 1.054 120 556 .422 1 130 4270 16490 68 81 395 408 0 6836 154 6681 .524 6994 6840 1.907 .529 -.932 -.92
16 7921 4103 135 122 7786 3981 8209 4202 137 124 8074 4080 0 0 1106 566 22 34 100 100 100 100 11767 12154 1.956 .511 .505 .512 .513 1.083 120 536 .508 .99 130 4440 16490 68 81 412 425 0 5065 151 4915 .631 5188 5037 1.584 .624 -.664 -.681
17 9927 3678 134 122 9793 3556 10380 3838 136 124 10246 3716 0 0 1868 614 23 21 100 100 100 100 13349 13962 2.754 .363 .363 .365 .362 1.083 120 518 .357 1 130 4610 16500 69 82 429 442 0 4541 151 4390 .448 4738 4588 2.231 .448 -1.157 -1.159
18 12191 6936 132 123 12059 6813 12787 7271 136 131 12655 7148 0 0 2228 1147 29 62 100 100 100 100 18872 19803 1.77 .565 .565 .567 .563 1.08 120 544 .555 .99 130 4780 16500 69 82 446 459 0 8563 152 8411 .697 8977 8825 1.434 .697 -.52 -.52
19 8734 6043 132 120 8602 5923 9169 6337 135 127 9037 6217 0 0 1475 956 29 60 100 100 100 100 14525 15254 1.452 .689 .688 .69 .687 1.085 120 574 .683 .99 130 4960 16490 68 81 464 477 0 7460 148 7312 .85 7823 7675 1.176 .849 -.234 -.236
20 2744 7467 131 119 2613 7348 2820 7489 132 120 2689 7370 0 0 435 1297 20 17 100 100 100 100 9961 10059 .356 2.812 2.741 2.813 2.826 1.098 120 558 2.817 .99 130 5140 16490 68 81 482 495 0 9219 147 9072 3.472 9246 9099 .288 3.384 1.796 1.759

Total number of rows: 16512

Table truncated, full table size 3767 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap