NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM30778 Query DataSets for GSM30778
Status Public on Sep 21, 2004
Title ENCODE: RNA PolII-IMR90 Rep1
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA using RNA polymerase II antibody
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name input DNA
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Genome-wide location analysis of RNA polymerase II binding at ENCODE regions in IMR90 cells. Replicate 1 of 3.
 
Submission date Sep 17, 2004
Last update date Nov 22, 2005
Contact name Chunxu Qu
E-mail(s) qchunxu@ucsd.edu
Phone (858)822-5767
Organization name Ludwig Institute for Cancer Research
Department Gene Regulation
Lab RenLab
Street address
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL1454
Series (1)
GSE1778 ENCODE: GWLA of TAF1, RNA PolII binding in four cell lines

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
SIGNIFICANCE significance
P-VAL p-value calculated using single array error model
F635_INT F635 intensity with background intensity subtracted
F532_INT F532 intensity with background intensity subtracted
F635_MEDIAN F635 mdian intensity
F635_MEAN F635 mean intensity
F635_SD F635 standard deviation
B635_MEDIAN B635 median intensity
B635_MEAN B635 mean intensity
B635_SD B635 standard deviation
F532_MEDIAN F532 median intensity
F532_MEAN F532 mean intensity
F532_SD F532 standard deviation
B532_MEDIAN B532 median intensity
B532_MEAN B532 mean intensity
B532_SD B532 standard deviation
FLAG flag from GenePro, 0 is useful
PRE_VALUE enrichment value (F635/F532)
UNF_VALUE log ratio (log2 of PRE_VALUE)

Data table
ID_REF VALUE SIGNIFICANCE P-VAL F635_INT F532_INT F635_MEDIAN F635_MEAN F635_SD B635_MEDIAN B635_MEAN B635_SD F532_MEDIAN F532_MEAN F532_SD B532_MEDIAN B532_MEAN B532_SD FLAG PRE_VALUE UNF_VALUE
1 0.8639383 0.3039 0.008303 368 202.27 428 446 164 60 69 42 421 435 129 129 132 38 0 1.82 0.8639383
2 0.8639383 0.3038 0.008316 472 258.77 535 546 210 63 72 42 502 505 177 129 132 37 0 1.82 0.8639383
3 0.8479973 0.3030 0.008461 579 322.24 642 638 235 63 72 43 592 589 175 128 131 38 0 1.80 0.8479973
4 0.8953033 0.3182 0.006063 535 288.06 595 601 204 60 70 45 544 539 170 129 131 36 0 1.86 0.8953033
5 0.8479973 0.3031 0.008447 500 277.60 564 581 215 64 71 40 527 531 146 127 129 36 0 1.80 0.8479973
6 0.7048723 0.0356 0.389548 321 196.69 387 605 1450 66 75 45 413 879 3146 129 131 37 0 1.63 0.7048723
7 0.8399603 0.2821 0.013081 238 133.22 303 323 145 65 76 46 321 326 99 128 131 38 0 1.79 0.8399603
8 -0.1681233 -0.0669 0.701063 364 410.82 429 437 166 65 74 43 719 720 168 128 130 36 0 0.89 -0.1681233
9 0.4750853 0.1761 0.082489 251 180.65 318 328 120 67 75 45 388 393 86 127 130 36 0 1.39 0.4750853
10 0.7739963 0.2381 0.030262 123 71.84 196 214 111 73 82 48 231 241 68 126 130 37 0 1.71 0.7739963
11 0.6040713 0.2178 0.042985 255 167.40 324 329 134 69 79 48 371 367 99 129 132 36 0 1.52 0.6040713
12 0.4436073 0.1714 0.088306 882 650.76 952 949 241 70 79 48 1065 1067 178 130 133 36 0 1.36 0.4436073
13 0.3334243 0.1303 0.152093 433 342.47 505 507 164 72 83 51 621 622 129 128 131 36 0 1.26 0.3334243
14 0.7655353 0.2657 0.018124 353 207.15 428 447 208 75 85 63 426 430 130 127 140 217 0 1.70 0.7655353
15 0.9107333 0.3009 0.008855 243 129.04 322 344 145 79 88 62 318 330 116 131 140 199 0 1.88 0.9107333
16 0.7824093 0.2802 0.013603 364 211.34 442 444 171 78 89 53 435 444 112 130 133 36 0 1.72 0.7824093
17 0.4222333 0.1556 0.109942 346 257.37 425 434 186 79 90 53 498 484 148 127 131 36 0 1.34 0.4222333
18 0.9560573 0.3083 0.007551 206 106.02 295 314 142 89 98 58 281 292 88 127 130 36 0 1.94 0.9560573
19 0.6870613 0.2462 0.026131 435 270.63 520 530 214 85 95 56 515 514 148 125 128 36 0 1.61 0.6870613
20 0.6959943 0.2502 0.024311 426 262.95 515 526 199 89 98 56 504 507 156 125 128 36 0 1.62 0.6959943

Total number of rows: 25392

Table truncated, full table size 2624 Kbytes.




Supplementary file Size Download File type/resource
GSM30778_cy3.tif.gz 53.7 Mb (ftp)(http) TIFF
GSM30778_cy5.tif.gz 52.7 Mb (ftp)(http) TIFF

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap