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Sample GSM93623 Query DataSets for GSM93623
Status Public on Jan 01, 2008
Title Mcm/ stationary phase/ replica 2
Sample type genomic
 
Channel 1
Source name ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, second replica
Organism Pyrococcus abyssi
Characteristics ChIP co-immunoprecipitated DNA using Mcm 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 Mcm 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 1.807 133 141 51 154 422 55 10 1 0 252 257 50 258 442 51 13 4 0 3.500 13.000 1.066 1.022 3.431 1.466 0.805 624 2230 -27 -14 -21 -6 -13 -1 0 1.807
2 -1.193 168 176 62 154 429 55 26 9 0 292 300 65 260 436 48 39 18 0 0.438 0.550 0.946 0.996 3.251 1.691 0.857 624 2250 46 62 14 32 22 40 0 -1.193
3 -0.148 386 402 137 145 421 51 94 89 0 520 530 136 253 430 49 95 91 0 0.903 0.928 0.924 0.903 1.755 2.412 0.501 460 2230 508 534 241 267 257 277 0 -0.148
4 0.385 85 90 39 132 287 47 2 0 0 192 196 38 228 376 44 2 0 0 1.306 1.313 1.250 1.278 2.798 0.661 0.387 624 2516 -83 -74 -47 -36 -42 -32 0 0.385
5 0.309 96 101 37 153 422 54 1 0 0 201 208 40 247 471 48 3 0 0 1.239 1.333 1.144 1.199 2.798 2.084 0.356 624 2473 -103 -91 -57 -46 -52 -39 0 0.309
6 0.170 193 235 132 157 578 53 44 31 0 289 337 135 257 680 49 43 31 0 1.125 0.975 0.988 0.997 3.168 0.958 0.668 624 2475 68 158 36 32 78 80 0 0.170
7 209 230 106 211 338 104 19 4 0 337 357 117 318 449 98 27 9 0 -0.105 0.487 1.003 1.006 2.881 0.604 0.296 624 2469 17 58 -2 19 19 39 -75
8 191 221 124 202 398 77 24 13 0 311 337 140 303 502 71 28 14 0 -1.375 0.559 1.000 1.019 3.084 0.536 0.213 624 2358 -3 53 -11 8 19 34 -75
9 398 715 700 179 465 66 79 66 0 491 812 701 282 485 62 80 66 0 1.048 1.011 1.032 1.016 2.396 0.958 0.767 624 2421 428 1066 219 209 536 530 -75 0.067
10 331 338 100 449 1002 211 0 0 0 415 429 99 520 1018 186 0 0 0 1.124 1.220 1.101 1.102 2.860 1.425 0.705 624 2416 -223 -202 -118 -105 -111 -91 -75 0.168
11 217 225 78 239 402 99 8 1 0 308 321 78 331 521 89 11 1 0 0.957 1.400 1.060 1.020 3.063 1.087 0.522 460 2365 -45 -24 -22 -23 -14 -10 -75 -0.064
12 395 640 590 158 285 58 84 71 0 497 753 607 255 363 53 86 75 0 0.979 0.968 1.007 0.978 2.506 1.477 0.499 460 2288 479 980 237 242 482 498 -75 -0.030
13 146 172 109 125 322 54 35 18 0 245 272 105 227 436 52 36 20 0 1.167 1.044 1.063 1.029 3.490 0.418 0.658 624 2559 39 92 21 18 47 45 -75 0.222
14 144 174 92 156 243 58 27 14 0 256 283 97 251 391 53 30 20 0 -2.400 0.563 0.943 1.018 2.936 0.261 0.506 624 2386 -7 50 -12 5 18 32 -75
15 338 582 579 147 309 56 65 58 0 427 686 574 246 439 51 72 61 0 1.055 0.989 1.005 1.010 2.572 0.542 0.773 624 2476 372 875 191 181 435 440 -75 0.078
16 225 249 131 312 522 111 5 2 0 319 337 112 397 567 103 5 1 0 1.115 1.050 1.074 1.090 3.002 0.981 0.270 624 2276 -165 -123 -87 -78 -63 -60 -75 0.158
17 289 316 131 340 674 113 10 4 0 356 387 135 415 704 102 12 5 0 0.864 0.857 0.964 0.883 3.346 1.263 0.431 624 2326 -110 -52 -51 -59 -24 -28 -75 -0.210
18 1217 2200 2253 240 742 96 87 79 0 1257 2224 2209 323 733 79 87 82 0 1.046 1.031 1.021 1.046 2.159 1.302 0.727 624 2368 1911 3861 977 934 1960 1901 -75 0.065
19 150 160 66 195 439 73 4 0 0 242 255 74 292 592 66 4 1 0 0.900 0.946 0.974 1.029 3.086 0.723 0.634 624 2209 -95 -72 -45 -50 -35 -37 -75 -0.152
20 145 152 56 165 345 61 9 1 0 243 252 56 266 465 58 9 2 0 0.870 0.929 1.054 1.015 3.160 1.095 0.552 624 2300 -43 -27 -20 -23 -13 -14 -75 -0.202

Total number of rows: 2304

Table truncated, full table size 400 Kbytes.




Supplementary data files not provided
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