Dataset Information

Effects of gene-by-environment interaction on the mRNA profile in the light of differential susceptibility

ABSTRACT: Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on mRNA expression in the context of differential susceptibility Methods: Following prenatal stress and behavioural screening in adulthood, month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). Following library preparation, samples were sequenced on the illumina HiSeq2000 platform (single end, 50 bp, 30 million reads/sample). Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). These counts were then used for the analysis of differentially expressed genes (DEGs) using the R package DeSeq2 (Love et al. 2014). Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct gene expression. As expected, the effect sizes and significances were rather subtle. Conclusion: the modulation of differential susceptibility seems to be modulated by distinct mRNA expression profiles, dependent on the serotonin transporter genotype

ORGANISM(S): Mus musculus

PROVIDER: GSE109929 | GEO | 2024/01/27

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on H3K4me3 enrichment in the context of differential susceptibility Methods: Following prenatal stress and behavioural screening in adulthood, 3 month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. For one of these portions the material was split again in two portions, of which one was fixed using 1% PFA, and was subsequently processed using a standard Chromatin immuno precipitation protocol. Following ChIP, the samples were processed by Nxt-Dx Belgium. Library preparation was performed using the NEBNext Ultra II DNA Library prep kit for Illumina (NEB, Ipswitch, Massatchusettes, USA). Subsequently, the whole IP material was subjected to ends prep and ligation of Illumina adaptors. A clean up of the adaptor-ligated DNA with AMPure XP beads (Beckman Coulter) was performed without size selection. The eluted material was subjected to enrichment PCR (14 cycles) with the NEBNext Index primers, and a last clean up with AMPure XP beads followed. The quality of the final libraries was checked on a Bioanalyzer 2100 DNA 1000 chip (Agilent, Santa Clara, CA, USA). The concentration was determined by performing qPCR on the samples using a dilution of PhiX index3 as standard. The concentration of all indexed samples was adjusted to 10 nM and samples were pooled for sequencing. Sequencing was performed on an Illumina HiSeq4000 (read-length of 50 bp with 25-30 million reads/sample, paired-end). Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct H3K4me3 enrichment. As expected, the effect sizes and significances were rather subtle. Conclusion: the epigenetic regulation by prenatal stress seems to be modulated by the serotonin transporter genotype

Dataset Information

Effects of gene-by-environment interaction on the mRNA profile in the light of differential susceptibility

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure