|
| Status |
Public on Feb 18, 2014 |
| Title |
Subtelomeric CTCF and Cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We investigated the reported binding of telomere associated factor TERF1 and TERF2 to internal telomere sites using ChIP-Seq for these two factors in a lymphoblastoid cell line. We mapped over 40 million reads for each sample to a custom reference genome that incorporates our subtelomere assembly, and generated signal tracks using only uniquely mapping reads, and also using a multimapping pipeline we developed. We find that peaks are misshapen and made up of reads that cannot be distinguished from true telomere sequence. Removing telomere identified reads removes all internal signal.
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| |
|
| Overall design |
Examination of TRF1 and TRF2
|
| |
|
| Contributor(s) |
Lieberman P |
| Citation(s) |
24676094 |
| |
| Submission date |
Feb 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Stong |
| E-mail(s) |
nstong@upenn.edu
|
| Organization name |
Wistar Institute/UPenn
|
| Street address |
3600 Spruce St
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
|
| Samples (3) |
|
| Relations |
| BioProject |
PRJNA238475 |
| SRA |
SRP038083 |
