NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM93617 Query DataSets for GSM93617
Status Public on Jan 01, 2008
Title Cdc 6/stationary phase replica 2
Sample type genomic
 
Channel 1
Source name ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, second replica
Organism Pyrococcus abyssi
Characteristics ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, second replica
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name DNA from mock-treated cell extract and archaebacteria treated in stationary phase, second replica
Organism Pyrococcus abyssi
Characteristics DNA from mock-treated cell extract and archaebacteria treated in stationary phase, second replica
Extracted molecule genomic DNA
Label Cy3
 
 
Description ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, second replica
Data processing Log base 2 ratio of median values of channel 1 to channel 2
 
Submission date Jan 24, 2006
Last update date Jan 24, 2007
Contact name LAWRENCE AGGERBECK
E-mail(s) [email protected], [email protected], [email protected]
Phone 33-(0)169823752
Fax 33-(0)169823740
Organization name Centre National de la Recherche Scientifique
Department Centre de Génétique Moléculaire
Lab GODMAP
Street address Avenue de la Terrasse

City Gif-sur-Yvette
ZIP/Postal code 91198
Country France
 
Platform ID GPL3384
Series (1)
GSE4104 Origin of replication for Pyrococcus abyssi by ChIP-chip

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
F635 Median ChIP co-immunoprecipitated DNA
F635 Mean ChIP co-immunoprecipitated DNA
F635 SD ChIP co-immunoprecipitated DNA
B635 Median ChIP co-immunoprecipitated DNA
B635 Mean ChIP co-immunoprecipitated DNA
B635 SD2 ChIP co-immunoprecipitated DNA
% > B635+1SD2 ChIP co-immunoprecipitated DNA
% > B635+2SD2 ChIP co-immunoprecipitated DNA
F635 % Sat. ChIP co-immunoprecipitated DNA
F532 Median DNA from mock-treated cell extract
F532 Mean DNA from mock-treated cell extract
F532 SD DNA from mock-treated cell extract
B532 Median DNA from mock-treated cell extract
B532 Mean DNA from mock-treated cell extract
B532 SD2 DNA from mock-treated cell extract
% > B532+1SD2 DNA from mock-treated cell extract
% > B532+2SD2 DNA from mock-treated cell extract
F532 % Sat. DNA from mock-treated cell extract
Ratio of Medians ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
Ratio of Means ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
Median of Ratios ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
Mean of Ratios ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
Ratios SD ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
Rgn Ratio ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
"Rgn R""d"
F Pixels Foreground pixels
B Pixels Background pixels
Sum of Medians ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
Sum of Means ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract
F635 Median - B635 ChIP co-immunoprecipitated DNA
F532 Median - B532 DNA from mock-treated cell extract
F635 Mean - B635 ChIP co-immunoprecipitated DNA
F532 Mean - B532 DNA from mock-treated cell extract
Flags -100, bad; - 75 empty; -50 not found; 0 good; 100 good by user
UNF_VALUE Value of log base 2 ratio of the background subtracted median value of the ChIP co-immunoprecipitated DNA to DNA from mock-treated cell extract

Data table
ID_REF VALUE F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD2 % > B635+1SD2 % > B635+2SD2 F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD2 % > B532+1SD2 % > B532+2SD2 F532 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio "Rgn R""d" F Pixels B Pixels Sum of Medians Sum of Means F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags UNF_VALUE
1 -0.585 111 117 43 127 383 53 8 1 0 175 197 67 199 514 58 17 6 0 0.667 5.000 0.771 0.721 3.587 0.600 0.568 392 2116 -40 -12 -16 -24 -10 -2 0 -0.585
2 -0.545 117 127 51 215 309 90 0 0 0 180 197 62 323 429 121 0 0 0 0.685 0.698 0.725 0.687 2.092 0.892 0.549 540 2085 -241 -214 -98 -143 -88 -126 0 -0.545
3 -0.525 270 296 111 172 321 79 60 27 0 391 436 154 250 454 97 72 29 0 0.695 0.667 0.673 0.673 2.366 0.790 0.340 460 2164 239 310 98 141 124 186 0 -0.525
4 -0.483 97 107 45 268 399 117 0 0 0 160 174 63 399 585 167 0 0 0 0.715 0.716 0.720 0.699 1.417 1.526 0.557 540 2356 -410 -386 -171 -239 -161 -225 0 -0.483
5 -0.413 100 108 46 248 391 82 0 0 0 161 178 71 358 581 106 1 0 0 0.751 0.778 0.770 0.770 1.659 1.038 0.765 540 2324 -345 -320 -148 -197 -140 -180 0 -0.413
6 -0.282 160 175 67 197 330 63 11 4 0 238 266 91 283 487 76 15 7 0 0.822 1.294 0.864 0.787 2.895 1.746 0.642 540 2362 -82 -39 -37 -45 -22 -17 0 -0.282
7 183 260 257 206 305 89 15 11 0 265 399 418 302 492 110 17 12 0 0.622 0.557 0.710 0.717 3.631 0.271 0.515 460 2212 -60 151 -23 -37 54 97 -75 -0.686
8 171 187 100 230 398 92 6 2 0 251 291 158 336 648 124 9 5 0 0.694 0.956 0.742 0.730 2.984 0.356 0.702 460 2258 -144 -88 -59 -85 -43 -45 -75 -0.527
9 228 289 203 188 330 79 40 25 0 306 398 274 255 478 100 38 26 0 0.784 0.706 0.790 0.790 2.980 0.352 0.721 540 2370 91 244 40 51 101 143 -75 -0.350
10 236 247 89 203 462 75 31 11 0 376 397 129 329 690 93 35 13 0 0.702 0.647 0.649 0.665 3.738 1.171 0.745 460 2346 80 112 33 47 44 68 -75 -0.510
11 183 192 69 210 401 70 11 2 0 301 322 114 337 595 95 12 5 0 0.750 1.200 0.745 0.688 3.358 0.663 0.299 460 2270 -63 -33 -27 -36 -18 -15 -75 -0.415
12 187 206 104 150 317 60 38 19 0 309 342 173 244 486 78 43 24 0 0.569 0.571 0.604 0.625 3.560 1.196 0.373 540 2330 102 154 37 65 56 98 -75 -0.813
13 223 268 199 200 273 94 24 13 0 302 381 317 271 379 124 27 15 0 0.742 0.618 0.740 0.638 3.845 0.405 0.160 392 2182 54 178 23 31 68 110 -75 -0.431
14 121 128 47 139 235 52 7 2 0 171 182 70 194 311 62 9 3 0 0.783 0.917 0.814 0.876 3.285 0.303 0.214 392 2274 -41 -23 -18 -23 -11 -12 -75 -0.354
15 272 498 511 120 220 45 75 62 0 417 771 811 185 329 60 73 59 0 0.655 0.645 0.667 0.730 2.935 0.610 0.644 392 2294 384 964 152 232 378 586 -75 -0.610
16 127 144 82 169 350 68 8 2 0 210 237 117 253 461 79 14 6 0 0.977 1.563 0.824 0.777 2.841 3.279 0.441 460 2292 -85 -41 -42 -43 -25 -16 -75 -0.034
17 198 208 80 206 376 82 13 2 0 299 323 109 302 525 101 21 6 0 2.667 0.095 0.714 0.712 3.447 2.343 0.389 460 2234 -11 23 -8 -3 2 21 -75 1.415
18 344 426 285 286 545 129 36 22 0 465 587 390 379 625 160 36 25 0 0.674 0.673 0.718 0.772 3.532 0.547 0.340 460 2173 144 348 58 86 140 208 -75 -0.568
19 260 349 292 240 353 89 26 18 0 345 496 428 334 549 116 29 19 0 1.818 0.673 0.661 0.711 3.473 0.638 0.512 540 2256 31 271 20 11 109 162 -75 0.862
20 200 315 322 219 320 80 24 17 0 299 474 464 328 462 106 27 20 0 0.655 0.658 0.633 0.643 3.203 0.700 0.642 540 2173 -48 242 -19 -29 96 146 -75 -0.610

Total number of rows: 2304

Table truncated, full table size 391 Kbytes.




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