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Sample GSM93616 Query DataSets for GSM93616
Status Public on Jan 01, 2008
Title Cdc 6/stationary phase
Sample type genomic
 
Channel 1
Source name ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, first replica
Organism Pyrococcus abyssi
Characteristics ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, first replica
Extracted molecule genomic DNA
Label Cy5
 
Channel 2
Source name DNA from mock-treated cell extract and archaebacteria treated in stationary phase, first 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 in stationary phase
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 -0.298 409 412 77 187 971 89 96 72 0 522 526 58 249 924 76 100 99 0 0.813 0.812 0.774 0.774 1.607 1.085 0.782 392 1999 495 502 222 273 225 277 0 -0.298
2 -0.426 359 362 66 138 592 62 99 94 0 499 503 60 202 545 52 100 99 0 0.744 0.744 0.750 0.721 1.475 1.077 0.799 316 2118 518 525 221 297 224 301 0 -0.426
3 -0.315 403 409 83 145 696 61 100 96 0 535 547 83 214 644 56 100 100 0 0.804 0.793 0.799 0.773 1.440 1.095 0.286 316 2126 579 597 258 321 264 333 0 -0.315
4 -0.828 286 286 70 237 630 86 27 4 0 404 402 80 317 762 80 52 16 0 0.563 0.576 0.711 0.699 3.109 0.532 0.394 540 2527 136 134 49 87 49 85 0 -0.828
5 -0.823 259 264 78 207 546 73 37 8 0 383 385 94 291 615 69 63 25 0 0.565 0.606 0.692 0.651 3.091 1.160 0.133 540 2489 144 151 52 92 57 94 0 -0.823
6 -1.133 289 294 72 258 663 89 18 2 0 408 414 89 340 745 88 40 7 0 0.456 0.486 0.762 0.702 3.278 1.253 0.547 540 2423 99 110 31 68 36 74 0 -1.133
7 237 533 517 193 582 79 46 40 0 303 637 652 268 774 72 45 40 0 1.257 0.921 1.006 0.952 2.574 0.645 0.669 540 2422 79 709 44 35 340 369 -75 0.330
8 227 447 411 180 466 72 47 42 0 274 533 432 253 563 66 45 42 0 2.238 0.954 0.978 0.974 3.050 0.275 0.361 540 2490 68 547 47 21 267 280 -75 1.162
9 230 453 427 209 637 87 40 36 0 297 555 466 274 738 75 41 37 0 0.913 0.868 1.034 0.974 2.990 0.808 0.275 540 2401 44 525 21 23 244 281 -75 -0.131
10 180 448 504 229 872 92 32 29 0 258 566 567 301 972 85 32 30 0 1.140 0.826 1.044 0.999 2.927 1.022 0.673 540 2221 -92 484 -49 -43 219 265 -75 0.188
11 166 343 318 186 635 71 37 32 0 245 460 377 258 702 62 39 35 0 1.538 0.777 0.918 0.915 2.708 1.242 0.742 540 2312 -33 359 -20 -13 157 202 -75 0.621
12 138 254 222 164 770 65 32 29 0 217 357 265 238 808 58 33 30 0 1.238 0.756 0.967 1.022 2.632 1.083 0.756 540 2274 -47 209 -26 -21 90 119 -75 0.308
13 170 300 306 121 348 73 44 35 0 235 395 339 194 472 63 44 37 0 1.195 0.891 0.959 0.987 3.041 0.413 0.601 540 2528 90 380 49 41 179 201 -75 0.257
14 154 208 163 172 382 74 30 19 0 224 296 172 245 501 69 35 26 0 0.857 0.706 0.951 0.922 2.729 0.247 0.485 540 2511 -39 87 -18 -21 36 51 -75 -0.222
15 147 209 153 184 618 78 28 20 0 231 312 180 263 769 78 30 26 0 1.156 0.510 0.944 0.943 2.716 0.291 0.400 540 2488 -69 74 -37 -32 25 49 -75 0.209
16 365 955 1401 623 4610 451 30 19 0 389 1053 1490 480 2763 270 39 35 0 2.835 0.579 1.427 1.263 2.500 2.437 0.603 540 2138 -349 905 -258 -91 332 573 -75 1.503
17 575 594 161 292 1894 197 71 28 0 716 731 153 283 1747 127 99 90 0 0.654 0.674 0.652 0.617 1.893 1.130 0.680 120 940 716 750 283 433 302 448 -75 -0.614
18 489 507 173 291 1900 214 43 9 0 602 619 183 293 1801 130 89 60 0 0.641 0.663 0.682 0.620 2.827 0.918 0.464 120 940 507 542 198 309 216 326 -75 -0.642
19 154 212 156 182 574 73 25 16 0 224 299 182 250 821 62 28 22 0 1.077 0.612 1.000 1.025 2.981 0.666 0.786 624 2080 -54 79 -28 -26 30 49 -75 0.107
20 187 260 196 219 414 91 28 20 0 279 375 300 303 574 93 30 22 0 1.333 0.569 0.897 0.862 2.880 0.626 0.492 624 2185 -56 113 -32 -24 41 72 -75 0.415

Total number of rows: 2304

Table truncated, full table size 403 Kbytes.




Supplementary data files not provided
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