|
| Status |
Public on Aug 10, 2016 |
| Title |
Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Histone deacetylase inhibitors are efficacious epigenetic-based therapies for some cancers and neurological disorders; however, these drugs inhibit multiple Hdacs and have detrimental effects on the pre- and post-natal skeleton. To better understand how Hdac inhibitors affect the skeleton, we focused on understanding the role of one of their targets, Hdac3, in endochondral bone formation by deleting it in immature murine chondrocyte micro masses with Adeno-Cre. Hdac3-deficient chondrocytes expressed higher levels of pro-inflammatory and matrix degrading genes (e.g., Il-6, Mmp3, Mmp13, Saa3) and lower levels of genes related to the extracellular matrix production, bone development and ossification (e.g., Acan, Col2a1, Ihh, Col10a1). Histone acetylation was increased in and around genes with elevated expression.
|
| |
|
| Overall design |
High Throughput RNA sequencing and Chromatin immunopreciptation sequencing experiments were performed in chondrocyte cultures. Differential analysis was conducted on ChIP-seq and RNA-seq data to identify H3K27Ac profile for up and down regulated genes in Hdac3-deficient murine chondrocytes.
|
| |
|
| Contributor(s) |
Westendorf J, Carpio L, Gaonkar K, Yan H, Nie J, Lee J |
| Citation(s) |
27507649 |
| |
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Jane Westendorf |
| E-mail(s) |
Westendorf.Jennifer@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Street address |
200 First Street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (4)
|
|
| This SubSeries is part of SuperSeries: |
| GSE75552 |
Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes |
|
| Relations |
| BioProject |
PRJNA304519 |
| SRA |
SRP066838 |
Less...
More...