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| Status |
Public on Sep 01, 2006 |
| Title |
FAIRE performed in human foreskin fibroblast cells |
| Project |
Pilot ENCODE
|
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters.
Keywords: Genome wide map of active chromatin
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| Overall design |
Human foreskin fibroblast (ATCC CRL 2091) cells were cultured in 245 x 245 cm plates (90% confluent). Formaldehyde was added directly to the plates at room temperature to a final concentration of 1%; and incubated for 1, 2, 4, or 7 minutes. Cells were glass bead disrupted and sheared using sonication, yielding fragments of DNA 0.5 to 1 kb. Proteins and DNA fragments crosslinked to proteins were removed using a phenol/chloroform extraction.
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| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Giresi PG, Kim J, Iyer VR, Lieb JD |
| Citation(s) |
17179217, 17571346 |
| BioProject |
PRJNA63415 |
| |
| Submission date |
May 22, 2006 |
| Last update date |
Sep 14, 2012 |
| Contact name |
Jason D Lieb |
| E-mail(s) |
jlieb@bio.unc.edu
|
| Phone |
919-843-3229
|
| URL |
http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Biology
|
| Lab |
Jason Lieb
|
| Street address |
203 Fordham Hall
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL3514 |
ENCODE NimbleGen hg17_04252005 tiling array |
|
| Samples (4)
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| GSM109841 |
FAIRE performed in human foreskin fibroblast cells crosslinked for 1 minute |
| GSM109842 |
FAIRE performed in human foreskin fibroblast cells crosslinked for 2 minute |
| GSM109843 |
FAIRE performed in human foreskin fibroblast cells crosslinked for 4 minutes |
| GSM109844 |
FAIRE performed in human foreskin fibroblast cells crosslinked for 7 minutes |
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