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Series GSE75547 Query DataSets for GSE75547
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
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)
GSM1958881 Cre-K27ac ChIP-Seq
GSM1958882 GFP-K27ac ChIP-Seq
GSM1958884 Cre Input ChIP-Seq
This SubSeries is part of SuperSeries:
GSE75552 Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes
BioProject PRJNA304519
SRA SRP066838

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Supplementary file Size Download File type/resource
GSE75547_RAW.tar 420.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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