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Sample GSM93620 Query DataSets for GSM93620
Status Public on Jan 01, 2008
Title Cdc 6/exponential phase replica 2
Sample type genomic
 
Channel 1
Source name ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, second replica
Organism Pyrococcus abyssi
Characteristics ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, second replica
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name DNA from mock-treated cell extract and archaebacteria treated in exponential phase, second replica
Organism Pyrococcus abyssi
Characteristics DNA from mock-treated cell extract and archaebacteria treated in exponential phase
Extracted molecule genomic DNA
Label Cy3
 
 
Description ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential 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 88 96 41 146 337 57 2 0 0 275 282 73 236 447 59 39 17 0 -1.487 -1.087 1.857 1.799 4.501 0.742 0.564 460 2084 -19 -4 -58 39 -50 46 0
2 88 93 34 139 323 56 1 0 0 277 279 64 233 407 64 35 9 0 -1.159 -1.000 1.406 1.312 4.816 0.872 0.534 460 2156 -7 0 -51 44 -46 46 0
3 97 103 39 166 407 66 0 0 0 287 297 79 259 514 74 24 4 0 -2.464 -1.658 2.587 2.491 4.118 0.891 0.422 460 2237 -41 -25 -69 28 -63 38 0
4 3.248 79 81 24 155 340 59 0 0 0 223 228 44 231 408 57 10 0 0 9.500 24.667 2.381 2.869 2.768 1.370 0.637 460 2361 -84 -77 -76 -8 -74 -3 0 3.248
5 0.653 80 86 33 231 481 79 0 0 0 219 225 47 315 595 81 0 0 0 1.573 1.611 1.547 1.727 1.996 1.544 0.722 540 2367 -247 -235 -151 -96 -145 -90 0 0.653
6 0.371 101 117 82 348 675 105 0 0 0 254 271 111 445 770 110 1 0 0 1.293 1.328 1.279 1.363 1.572 1.096 0.593 540 2413 -438 -405 -247 -191 -231 -174 0 0.371
7 176 183 83 218 464 85 9 1 0 269 294 114 319 653 99 12 4 0 0.840 1.400 0.803 0.773 2.937 0.582 0.650 540 2360 -92 -60 -42 -50 -35 -25 -75 -0.252
8 188 204 98 223 359 86 12 4 0 284 317 140 317 521 96 19 8 0 1.061 100000.000 0.789 0.800 3.385 0.401 0.716 540 2357 -68 -19 -35 -33 -19 0 -75 0.085
9 115 127 59 160 285 61 5 1 0 211 225 77 245 447 66 10 2 0 1.324 1.650 0.938 0.903 2.891 0.259 0.748 460 2420 -79 -53 -45 -34 -33 -20 -75 0.404
10 135 203 163 224 605 89 20 14 0 225 315 203 317 767 97 23 18 0 0.967 10.500 0.877 0.859 2.361 0.937 0.788 540 2337 -181 -23 -89 -92 -21 -2 -75 -0.048
11 143 195 139 197 515 85 22 13 0 222 298 168 286 652 94 26 16 0 0.844 -0.167 0.840 0.815 2.492 1.045 0.580 460 2305 -118 10 -54 -64 -2 12 -75 -0.245
12 150 165 79 224 535 96 4 1 0 239 266 108 314 655 105 8 2 0 0.987 1.229 0.897 0.873 2.433 0.962 0.686 540 2341 -149 -107 -74 -75 -59 -48 -75 -0.019
13 204 227 118 197 327 85 27 11 0 280 325 151 280 434 94 32 16 0 100000.000 0.667 0.776 0.740 3.021 0.688 0.228 392 2308 7 75 7 0 30 45 -75 16.610
14 166 183 83 205 360 95 9 1 0 272 289 108 297 487 103 13 3 0 1.560 2.750 0.966 0.977 3.374 0.744 0.245 392 2348 -64 -30 -39 -25 -22 -8 -75 0.642
15 157 172 77 180 334 71 13 4 0 242 267 102 268 459 76 17 7 0 0.885 8.000 0.800 0.851 3.276 0.578 0.070 392 2364 -49 -9 -23 -26 -8 -1 -75 -0.177
16 288 309 123 344 712 133 9 1 0 405 443 167 460 821 158 13 4 0 1.018 2.059 0.911 0.882 3.376 1.233 0.479 460 2232 -111 -52 -56 -55 -35 -17 -75 0.026
17 190 211 99 268 478 119 5 1 0 294 328 133 367 608 127 10 3 0 1.068 1.462 0.911 0.923 2.969 0.815 0.442 460 2234 -151 -96 -78 -73 -57 -39 -75 0.096
18 157 194 122 202 529 102 12 5 0 258 303 169 298 683 112 14 7 0 1.125 -1.600 0.819 0.817 2.902 0.994 0.264 460 2191 -85 -3 -45 -40 -8 5 -75 0.170
19 221 239 100 260 326 92 10 4 0 342 371 135 360 492 110 18 8 0 2.167 -1.909 0.935 0.928 4.015 0.567 0.288 460 2220 -57 -10 -39 -18 -21 11 -75 1.115
20 151 166 71 274 557 110 1 0 0 252 275 107 372 718 122 3 0 0 1.025 1.113 0.972 0.994 2.435 0.893 0.742 540 2262 -243 -205 -123 -120 -108 -97 -75 0.036

Total number of rows: 2304

Table truncated, full table size 391 Kbytes.




Supplementary data files not provided
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