NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM171034 Query DataSets for GSM171034
Status Public on Mar 01, 2007
Title TAFII p250 (6B3) GM06990 RenLab ENCODE PCR tiling array replicate 1 ENC1526
Sample type genomic
 
Channel 1
Source name Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody
Organism Homo sapiens
Characteristics Chromatin immunoprecipitated DNA from GM06990 cells using TAFII p250 (6B3) antibody
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy5
Label protocol Cy3 input Cy5 ChIP sample
 
Channel 2
Source name Input DNA from GM06990 cells
Organism Homo sapiens
Characteristics Input DNA from GM06990 cells
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM06990
Extracted molecule genomic DNA
Extraction protocol NimbleGen
Label Cy3
Label protocol Cy3 input Cy5 ChIP sample
 
 
Hybridization protocol NimbleGen
Scan protocol NimbleGen
Description ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
Data processing raw data
 
Submission date Feb 23, 2007
Last update date Aug 28, 2007
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Department Department of Cellular and Molecular Medicine
Lab Laboratory of Gene Regulation
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platform ID GPL1454
Series (1)
GSE7118 Ludwig Institute/UCSD ENCODE project March 2007 Release

Data table header descriptions
ID_REF ID_REF
VALUE same as UNF_VALUE but with flagged values removed
STATISTICS statistics
PVAL p-value
F635_INT F635 intensity with background intensity subtracted (normalized)
F532_INT F532 intensity with background intensity subtracted (normalized)
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 F532standard deviation
B532_MEDIAN B532 median intensity
B532_MEAN B532 mean intensity
B532_SD B532 standard deviation
FLAG flag from GenePro, 0 is useful
UNF_VALUE log ratio (F635/F532)

Data table
ID_REF VALUE STATISTICS PVAL 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 UNF_VALUE
1 -0.109 0.98 5.300e-01 933.00 948.98 1008 1017 348 75 92 76 1178 1157 322 172 174 59 0 -0.109
2 -0.125 0.97 5.484e-01 752.00 773.52 828 833 374 76 92 76 989 981 334 169 172 59 0 -0.125
3 -0.583 0.71 9.328e-01 2018.00 2850.72 2095 2046 723 77 94 82 3195 3061 993 173 178 96 0 -0.583
4 -0.632 0.68 9.509e-01 1125.00 1645.15 1202 1241 393 77 93 75 1918 1903 476 174 177 65 0 -0.632
5 -0.582 0.71 9.349e-01 1254.00 1770.62 1331 1357 382 77 92 74 2052 2019 512 175 176 62 0 -0.582
6 -0.109 0.98 5.308e-01 2672.00 2717.71 2751 2721 710 79 108 322 3055 3051 421 174 182 113 0 -0.109
7 -0.595 0.70 9.417e-01 1729.00 2463.96 1807 1853 528 78 109 330 2785 2732 440 173 180 112 0 -0.595
8 -0.768 0.62 9.788e-01 632.00 1015.01 707 710 264 75 92 77 1247 1244 262 171 173 57 0 -0.768
9 -0.819 0.60 9.852e-01 953.00 1585.72 1032 1072 377 79 96 78 1853 1903 373 172 174 58 0 -0.819
10 -0.770 0.62 9.796e-01 734.00 1181.04 812 851 289 78 95 75 1425 1429 273 173 173 57 0 -0.770
11 -0.960 0.55 9.939e-01 941.00 1726.28 1020 1028 403 79 95 74 2004 1919 557 174 176 58 0 -0.960
12 -0.756 0.63 9.774e-01 1913.00 3046.93 1993 1941 704 80 94 75 3403 3244 797 173 176 59 0 -0.756
13 -0.264 0.88 7.142e-01 1198.00 1357.44 1280 1286 363 82 95 74 1613 1622 215 174 176 58 0 -0.264
14 -0.381 0.81 8.218e-01 5345.00 6566.47 5428 5153 1444 83 121 909 7135 6853 1682 174 179 80 0 -0.381
15 -0.449 0.78 8.711e-01 1053.00 1355.55 1133 1165 331 80 95 74 1612 1622 233 175 177 58 0 -0.449
16 -0.570 0.71 9.339e-01 1524.00 2134.74 1603 1603 402 79 94 75 2435 2428 281 172 174 60 0 -0.570
17 -0.441 0.78 8.610e-01 803.00 1028.22 884 875 343 81 97 77 1265 1219 299 175 178 63 0 -0.441
18 -0.887 0.57 9.910e-01 2224.00 3880.83 2310 2323 760 86 100 77 4290 4228 924 176 178 57 0 -0.887
19 1.06 4.803e-01 10.00 9.43 79 91 70 85 101 79 174 178 54 181 181 57 -50 -0.222
20 -0.340 0.84 7.910e-01 7900.00 9434.17 7979 7947 1323 79 99 82 10180 10093 1220 179 179 57 0 -0.340

Total number of rows: 25246

Table truncated, full table size 2389 Kbytes.




Supplementary file Size Download File type/resource
GSM171034.gpr.gz 2.0 Mb (ftp)(http) GPR

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