|
| Status |
Public on Jan 20, 2007 |
| Title |
E2F4 and Myc ChIP-chip perfomed on Nimblegen hg17 ENCODE arrays |
| Project |
Pilot ENCODE
|
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. ChIP-chip is a powerful technique to map chromosomal targets of transcription factors. We applied ChIP-chip to map downstream targets of the transcription factor E2F4 and c-Myc. E2F4 is a member of the E2F family of transcriptional regulators that functions as a repressor in quiescent and early G1 cells. c-Myc is a oncogenic transcription factor implicated in almost all aspects of tumorigenesis. We mapped E2F4 and c-Myc binding sites in 1% of the human genome using Nimblegen hg17 ENCODE arrays.
Keywords: ChIP-chip
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| Overall design |
Cultured cells are cross-linked in vivo using 1% formaldehyde and chromatin is sheared to less than 1 kb fragments using a sonicator. Specific protein-dna complexes are pulled down using a specific antibody. After adequate washing, the protein-dna complexes are eluted, reverse cross-linked and the DNA purified by phenol-chloroform extraction. ChIP-enriched DNA is now labeled with Cy5 while DNA derived from a mock IP is used as a reference and labeled with Cy3. Samples are then hybridized on ENCODE arrays.
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| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Kim J, Bhinge A, Iyer V, Singer M, Jiang N, Green R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63421 |
| |
| Submission date |
Nov 27, 2006 |
| Last update date |
Jun 28, 2012 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
iyerlab@gmail.com
|
| Phone |
5122327833
|
| Organization name |
University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway Dr. MBB 3.212
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL3514 |
ENCODE NimbleGen hg17_04252005 tiling array |
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| Samples (12)
|
| GSM147141 |
E2F4 chip-chip in serum starved 2091 fibroblasts replicate 1 |
| GSM147142 |
E2F4 chip-chip in serum starved 2091 fibroblasts replicate 2 |
| GSM147143 |
E2F4 chip-chip in serum starved 2091 fibroblasts replicate 3 |
| GSM147292 |
Myc ChIP-chip in serum starved fibroblasts set 1 |
| GSM147322 |
Myc ChIP-chip in serum starved fibroblasts set 2 |
| GSM147323 |
Myc ChIP-chip in serum starved fibroblasts set 3 |
| GSM147324 |
Myc ChIP-chip in serum stimulated fibroblasts set 1 |
| GSM147325 |
Myc ChIP-chip in serum stimulated fibroblasts set 2 |
| GSM147326 |
Myc ChIP-chip in serum stimulated fibroblasts set 3 |
| GSM147327 |
Myc ChIP-chip in HeLa cells replicate 1 |
| GSM147328 |
Myc ChIP-chip in HeLa cells replicate 2 |
| GSM147329 |
Myc ChIP-chip in HeLa cells replicate 3 |
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