|
Status |
Public on Jan 01, 2007 |
Title |
Ludwig Institute/UCSD ENCODE project |
Project |
Pilot ENCODE
|
Organism |
Homo sapiens |
Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
Summary |
The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication. Keywords: ChIP-chip
|
|
|
Overall design |
ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
|
Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
|
|
|
Contributor(s) |
Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Heintzman ND, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K |
Citation missing |
Has this study been published? Please login to update or notify GEO. |
BioProject |
PRJNA63415 |
|
Submission date |
Nov 15, 2006 |
Last update date |
Jun 28, 2012 |
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 |
|
|
Platforms (1) |
GPL1454 |
RenLab ENCODE PCR tiling array |
|
Samples (24)
|
|