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| Status |
Public on Feb 28, 2014 |
| Title |
Role of DNA methylation in modulating transcription factor occupancy |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
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| Summary |
This data includes regulatory factor profiling using DNase and ChIP-seq and methylation profiling using bisulfite-seq.
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| Overall design |
We investigated CTCF occupancy in the context of reduced methylation by performing genome-wide profiling with chromatin immunoprecipitation (ChIP-seq) in HCT116 cells and DNMT1 and DNMT3B double knockout (DKO) HCT116 cells. We also profiled HCT116 and DKO using DNaseI-seq and ChIP-seq for trimethylation of histone 3 lysine 4 (H3K4me3) and acetylation of histone 3 lysine 27 (H3K27ac), Finally, we performed ChIP-seq on 3 replicates of mock-treated and 2 replicates of 5-aza-CdR-treated K562 cells.
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| Contributor(s) |
Maurano MT, Wang H, Stamatoyannopoulos JA |
| Citation(s) |
26257180 |
| |
| Submission date |
Sep 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew T Maurano |
| E-mail(s) |
maurano@nyu.edu
|
| Organization name |
NYU School of Medicine
|
| Department |
Institute for Systems Genetics
|
| Lab |
Maurano
|
| Street address |
435 East 30th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA218088 |
| SRA |
SRP029595 |
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