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Sample GSM93565 Query DataSets for GSM93565
Status Public on Jan 01, 2008
Title Cdc 6/puromycin
Sample type genomic
 
Channel 1
Source name ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria treated with puromycin, fourth replica
Organism Pyrococcus abyssi
Characteristics ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria treated with puromycin, fourth replica
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name DNA from mock-treated cell extract and archaebacteria treated with puromycin, fourth replica
Organism Pyrococcus abyssi
Characteristics DNA from mock-treated cell extract
Extracted molecule genomic DNA
Label Cy3
 
 
Description ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria treated with puromycin
Data processing Log base 2 ratio of median values of channel 1 to channel 2
 
Submission date Jan 23, 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 -2.780 154 158 55 139 404 57 20 4 0 341 359 92 238 419 58 78 43 0 0.146 0.157 0.316 0.326 3.241 1.090 0.422 392 2152 118 140 15 103 19 121 0 -2.780
2 -4.129 137 219 390 131 359 53 22 10 0 332 425 462 227 399 53 77 49 0 0.057 0.444 0.326 0.341 3.824 1.795 0.512 460 2140 111 286 6 105 88 198 0 -4.129
3 -2.273 162 196 221 138 362 57 31 13 0 341 392 275 225 443 56 84 52 0 0.207 0.347 0.378 0.332 2.859 0.952 0.582 460 2215 140 225 24 116 58 167 0 -2.273
4 -0.071 111 124 59 546 1013 174 0 0 0 259 271 70 716 1201 202 0 0 0 0.952 0.948 0.950 0.941 1.258 1.470 0.754 460 2387 -892 -867 -435 -457 -422 -445 0 -0.071
5 0.307 94 98 35 261 566 86 0 0 0 261 269 59 396 731 96 1 0 0 1.237 1.283 1.235 1.277 1.617 1.459 0.723 460 2384 -302 -290 -167 -135 -163 -127 0 0.307
6 1.246 117 120 39 200 471 69 0 0 0 284 289 50 319 625 75 2 0 0 2.371 2.667 1.817 2.047 2.746 1.192 0.790 540 2475 -118 -110 -83 -35 -80 -30 0 1.246
7 228 491 480 205 535 86 46 42 0 319 650 582 292 722 91 45 43 0 0.852 0.799 0.865 0.782 2.440 0.483 0.391 540 2357 50 644 23 27 286 358 -75 -0.231
8 239 454 454 170 384 72 49 46 0 274 598 569 252 566 77 46 44 0 3.136 0.821 0.928 0.930 2.548 0.439 0.307 540 2271 91 630 69 22 284 346 -75 1.649
9 335 580 569 195 378 81 53 48 0 374 735 698 268 514 80 51 49 0 1.321 0.824 0.911 0.929 2.532 0.686 0.492 460 2330 246 852 140 106 385 467 -75 0.401
10 161 485 581 191 415 66 35 32 0 256 763 878 310 607 78 35 32 0 0.556 0.649 0.762 0.704 2.641 0.820 0.346 540 2293 -84 747 -30 -54 294 453 -75 -0.848
11 165 460 506 147 465 57 44 40 0 245 669 699 239 674 60 43 41 0 3.000 0.728 0.781 0.731 2.824 0.775 0.761 540 2330 24 743 18 6 313 430 -75 1.585
12 142 303 285 136 373 54 43 39 0 226 471 403 226 490 57 43 40 0 100000.000 0.682 0.799 0.788 2.539 0.945 0.395 460 2314 6 412 6 0 167 245 -75 16.610
13 207 463 514 137 400 59 51 43 0 278 615 650 213 583 57 50 46 0 1.077 0.811 0.888 0.890 3.046 0.293 0.220 460 2404 135 728 70 65 326 402 -75 0.107
14 198 505 495 224 437 84 41 39 0 276 665 637 312 602 88 42 40 0 0.722 0.796 0.834 0.832 2.379 0.553 0.560 460 2333 -62 634 -26 -36 281 353 -75 -0.469
15 225 428 367 221 547 79 43 40 0 324 591 483 371 815 120 40 36 0 -0.085 0.941 0.705 0.690 2.435 0.372 0.598 460 2455 -43 427 4 -47 207 220 -75
16 326 606 594 218 825 91 52 45 0 395 784 760 312 886 93 48 43 0 1.301 0.822 0.825 0.843 2.948 1.296 0.431 540 2344 191 860 108 83 388 472 -75 0.380
17 263 512 513 189 904 82 49 43 0 332 681 661 277 937 84 46 42 0 1.345 0.800 0.778 0.769 3.093 1.124 0.211 540 2322 129 727 74 55 323 404 -75 0.428
18 584 940 1762 182 868 80 76 66 0 616 928 1152 257 877 79 69 62 0 1.120 1.130 0.937 1.032 3.560 1.199 0.394 540 2329 761 1429 402 359 758 671 -75 0.163
19 250 425 331 243 422 86 41 39 0 348 595 431 351 640 98 43 40 0 -2.333 0.746 0.772 0.768 2.724 0.697 0.533 460 2215 4 426 7 -3 182 244 -75
20 249 621 625 253 360 86 41 37 0 322 806 775 351 573 86 42 38 0 0.138 0.809 0.846 0.802 2.507 0.719 0.550 540 2192 -33 823 -4 -29 368 455 -75 -2.858

Total number of rows: 2304

Table truncated, full table size 397 Kbytes.




Supplementary data files not provided
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