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Sample GSM93621 Query DataSets for GSM93621
Status Public on Jan 01, 2008
Title Cdc 6/exponential phase replica 4
Sample type genomic
 
Channel 1
Source name ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, fourth replica
Organism Pyrococcus abyssi
Characteristics ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, fourth replica
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name DNA from mock-treated cell extract and archaebacteria treated in exponential phase, fourth 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, fourth 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 1.336 63 65 23 116 203 49 0 0 0 244 257 54 265 421 81 7 0 0 2.524 6.375 1.341 1.433 2.627 0.354 0.599 316 2073 -74 -59 -53 -21 -51 -8 0 1.336
2 67 71 26 107 251 43 0 0 0 254 264 57 240 526 72 18 3 0 -2.857 -1.500 1.436 1.354 4.180 0.459 0.706 460 2138 -26 -12 -40 14 -36 24 0
3 83 84 30 101 164 37 4 0 0 275 289 72 237 338 68 32 14 0 -0.474 -0.327 0.538 0.524 4.993 0.521 0.423 460 2100 20 35 -18 38 -17 52 0
4 -0.853 79 85 36 182 265 68 0 0 0 231 243 59 417 525 127 0 0 0 0.554 0.557 0.557 0.584 1.642 0.745 0.787 540 2359 -289 -271 -103 -186 -97 -174 0 -0.853
5 -0.858 73 76 25 254 347 84 0 0 0 230 237 51 558 718 147 0 0 0 0.552 0.555 0.556 0.557 1.228 0.625 0.533 460 2290 -509 -499 -181 -328 -178 -321 0 -0.858
6 -0.773 78 84 31 243 338 105 0 0 0 245 261 76 527 666 201 0 0 0 0.585 0.598 0.590 0.614 1.432 0.900 0.418 540 2429 -447 -425 -165 -282 -159 -266 0 -0.773
7 99 121 78 145 192 56 12 5 0 231 280 159 303 423 91 19 7 0 0.639 1.043 0.581 0.539 2.904 0.103 0.259 460 2252 -118 -47 -46 -72 -24 -23 -75 -0.646
8 121 135 74 127 189 49 23 9 0 273 302 166 272 408 90 30 14 0 -6.000 0.267 0.496 0.494 3.419 0.118 0.365 392 2251 -5 38 -6 1 8 30 -75
9 114 140 85 125 221 50 27 16 0 250 310 179 257 459 80 38 24 0 1.571 0.283 0.538 0.496 2.878 0.144 0.207 392 2306 -18 68 -11 -7 15 53 -75 0.652
10 106 122 66 131 255 51 15 5 0 257 295 151 295 515 87 21 9 0 0.658 100000.000 0.502 0.495 3.174 0.591 0.520 392 2162 -63 -9 -25 -38 -9 0 -75 -0.604
11 103 120 91 132 231 52 11 3 0 239 288 266 289 453 92 15 7 0 0.580 12.000 0.541 0.529 3.241 0.649 0.345 540 2270 -79 -13 -29 -50 -12 -1 -75 -0.786
12 80 90 47 104 240 42 9 3 0 191 224 108 227 485 70 19 7 0 0.667 4.667 0.584 0.603 3.244 1.026 0.708 460 2314 -60 -17 -24 -36 -14 -3 -75 -0.585
13 110 135 89 78 140 38 45 29 0 236 303 190 180 303 71 46 32 0 0.571 0.463 0.453 0.499 3.201 0.415 0.601 392 2206 88 180 32 56 57 123 -75 -0.807
14 93 109 77 111 148 42 14 6 0 214 255 163 255 370 76 17 8 0 0.439 100000.000 0.478 0.473 3.071 0.153 0.094 392 2250 -59 -2 -18 -41 -2 0 -75 -1.188
15 76 84 46 98 146 37 9 3 0 189 215 102 227 311 62 16 6 0 0.579 1.167 0.532 0.520 3.183 0.159 0.060 392 2354 -60 -26 -22 -38 -14 -12 -75 -0.788
16 127 134 59 160 334 69 6 1 0 290 315 132 350 611 124 10 3 0 0.550 0.743 0.557 0.573 3.213 0.526 0.395 460 2167 -93 -61 -33 -60 -26 -35 -75 -0.862
17 129 145 80 144 317 66 16 7 0 287 338 182 306 603 117 22 11 0 0.789 0.031 0.514 0.499 3.796 0.611 0.436 460 2161 -34 33 -15 -19 1 32 -75 -0.341
18 155 196 138 138 439 68 33 22 0 325 423 288 301 744 122 36 24 0 0.708 0.475 0.500 0.502 3.123 0.594 0.659 460 2169 41 180 17 24 58 122 -75 -0.497
19 97 107 47 152 181 64 3 0 0 238 267 114 351 431 129 5 1 0 0.487 0.536 0.463 0.464 2.675 0.410 0.414 540 2113 -168 -129 -55 -113 -45 -84 -75 -1.039
20 109 129 76 144 196 61 15 6 0 253 311 183 334 494 123 18 8 0 0.432 0.652 0.491 0.508 2.890 0.169 0.404 540 2119 -116 -38 -35 -81 -15 -23 -75 -1.211

Total number of rows: 2304

Table truncated, full table size 389 Kbytes.




Supplementary data files not provided
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