Dataset features

Specifications


Application: ChIP-seq analysis, BS-seq analysis, RNA-seq analysis
Number of samples: 33
Release date: Nov 5 2014
Last update date: Oct 24 2018
Access: Public
Diseases: Deficiency Diseases
Chemicals: 5-Methylcytosine
Genes: DNMT3A
Dataset link Epigenetic and transcriptional landscapes of Dnmt3a-deficient olfactory sensory neurons

Experimental Protocol


To determine the contributions of Dnmt3a to the DNA modification and transcriptional landscapes of a post-mitotic neuronal population, we performed DNA immunoprecipitation (DIP-seq) using antibodies specific for 5mC and 5hmC and rRNA-depleted transcriptional profiling (RNA-seq) coupled to high-throughput sequencing using genomic DNA or RNA from FACS-isolated mature olfactory sensory neurons (mOSNs) from main olfactory epithelium (MOE) of Dnmt3a wildtype (WT), heterozygous-null (Het), or homozygous-null (KO) 3-week old mice. Similarly, to compare this information with other epigenetic features of the MOE, we performed H3K4me1 (WT), H3K27ac (WT), and H3K27me3 (WT and KO) chromatin immunoprecipitation (ChIP)-seq and DNase I hypersensitivity assays (DNase-seq) using MOE nuclei from 3-week old mice. In addition, we assayed the influence of Dnmt3a-deficiency on the induction of odorant-responsive genes by exposing 3-week old Dnmt3a WT, Het, and KO mice to either water or a 1:1:1 mixture of amyl acetate:acetophenone:octanal for 1 hour and performed rRNA-depleted RNA-seq using RNA isolated from their MOEs.

Repositories


GEO

GSE52464

ArrayExpress

E-GEOD-52464

ENA

SRP033096

BioProject

PRJNA229056

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Contact


Stavros Lomvardas