NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM30787 Query DataSets for GSM30787
Status Public on Sep 21, 2004
Title ENCODE: RNA PolII-THP1 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 THP1 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 0.6690273 0.2477 0.039769 837 525.90 914 946 393 75 93 76 505 499 127 182 185 49 0 1.59 0.6690273
2 0.4222333 0.1625 0.124964 1036 773.29 1115 1151 420 77 96 76 656 635 173 182 184 49 0 1.34 0.4222333
3 0.5058913 0.1996 0.078860 2356 1654.71 2436 2444 581 78 97 76 1195 1170 274 183 187 49 0 1.42 0.5058913
4 0.6870613 0.2575 0.034159 1113 691.37 1189 1228 423 74 94 74 606 615 173 182 186 47 0 1.61 0.6870613
5 0.5260693 0.2018 0.076545 1216 842.10 1291 1339 497 73 94 73 696 678 187 180 182 47 0 1.44 0.5260693
6 0.7048723 0.2576 0.034123 1169 719.22 1246 1218 542 75 96 77 621 638 207 180 183 48 0 1.63 0.7048723
7 0.7136963 0.2569 0.034466 529 322.75 603 610 285 72 91 73 380 391 101 181 184 47 0 1.64 0.7136963
8 0.2016343 0.0774 0.291797 1279 1115.70 1356 1310 473 75 91 70 865 819 276 182 184 48 0 1.15 0.2016343
9 0.0840643 0.0346 0.403159 457 429.24 534 554 240 75 92 70 443 443 137 179 183 49 0 1.06 0.0840643
10 0.6690273 0.2299 0.051780 268 168.75 345 343 190 75 90 65 283 291 76 178 180 47 0 1.59 0.6690273
11 0.0840643 0.0306 0.414168 476 450.54 554 584 249 76 94 74 451 449 102 174 180 54 0 1.06 0.0840643
12 0.1110313 0.0468 0.370119 2060 1898.82 2138 2035 655 76 95 74 1340 1262 337 179 181 47 0 1.08 0.1110313
13 0.0976113 0.0374 0.395560 907 848.65 984 1020 413 75 95 75 704 696 200 184 186 49 0 1.07 0.0976113
14 0.6322683 0.2397 0.044841 1311 843.74 1391 1440 509 78 98 80 700 688 200 183 185 48 0 1.55 0.6322683
15 0.5558163 0.2061 0.072240 625 425.96 706 711 309 79 98 77 444 442 114 182 185 46 0 1.47 0.5558163
16 0.5558163 0.2115 0.067192 848 575.05 927 935 373 77 96 74 538 547 123 185 187 48 0 1.47 0.5558163
17 0.1375043 0.0535 0.352364 862 784.76 939 938 316 75 97 78 665 667 160 184 187 49 0 1.10 0.1375043
18 0.4329593 0.1603 0.128282 468 347.32 546 593 262 76 96 77 394 401 96 180 183 47 0 1.35 0.4329593
19 0.4329593 0.1694 0.115183 2281 1690.75 2358 2325 675 75 95 76 1210 1199 269 176 179 49 0 1.35 0.4329593
20 0.4222333 0.1666 0.119191 1297 964.97 1376 1360 414 77 96 74 771 742 199 180 185 49 0 1.34 0.4222333

Total number of rows: 25392

Table truncated, full table size 2615 Kbytes.




Supplementary file Size Download File type/resource
GSM30787.tif.gz 112.5 Mb (ftp)(http) TIFF

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