|
| Status |
Public on Jan 01, 2007 |
| Title |
U937_NONE_CTCF_ENC13152631 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Chromatin immunoprecipitated DNA from U937 cells using CTCF antibody
|
| Organism |
Homo sapiens |
| Characteristics |
cells: U937
|
| Extracted molecule |
genomic DNA |
| Label |
Cy5
|
| |
|
| Channel 2 |
| Source name |
input chromatin DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cells: U937
|
| Extracted molecule |
genomic DNA |
| Label |
Cy3
|
| |
|
| |
| Description |
For the PCR genome tiling ENCODE arrays, three independent CTCF ChIP-on-chip experiments were performed with U937 chromatin.
|
| Data processing |
The resulting array data were normalized by intensity-dependent loess (Dudoit et al.) and averaged, and probability statistics was calculated for each probe based on a single-error model described previously (Li et al., 2003). A stringent statistical threshold (P<1X10-6) was set to obtain a similar number of CTCF binding sites as detected in IMR90 cells to facilitate comparison between the two cell types. The resulting list of target sites were converted to NCBI35 (hg17) build of the human genome using the batch liftOver function available from the UCSC genome browser (Kent et al., 2002). A total of 257 CTCF binding sites were identified within the ENCODE region in U937 cells.
|
| |
|
| Submission date |
Aug 18, 2006 |
| Last update date |
Aug 23, 2006 |
| 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) |
| GSE5559 |
Analysis of the vertebrate insulator protein CTCF binding sites in the human genome |
|
