Genome wide identification of enhancer regions in the retrosplenial cortex of the prairie vole, Microtus ochrogaster.
Ontology highlight
ABSTRACT:
ORGANISM(S): Microtus ochrogaster
PROVIDER: GSE73670 | GEO | 2015/12/11
SECONDARY ACCESSION(S): PRJNA297599
REPOSITORIES: GEO
Similar Datasets
Project description:We use ChIP-seq targeting histone 3 lysine 4 mono-methylation (H3K4me1) to identify putative enhancer sites genome-wide, in the retrosplenial cortex of adult prairie vole males. ChIP samples were generated by targeting a known enhancer mark (H3K4me1) in chromatin extracted from the retrosplenial cortex of 8 males. Illumina libraries were prepared from ChIP and INPUT DNA and sequenced on Illimuna HiSeq 2500 platform.
2015-12-11 | E-GEOD-73670 | biostudies-arrayexpress
Project description:prairie vole gut metagenome pilot, raw sequence reads and assembly
| PRJNA449069 | ENA
Project description:This dataset contains RNA sequencing results from adult male prairie voles that were in either opposite-sex or same-sex pairs that were subsequently either separated from or remained paired with their partner for either 48 hours or 4 weeks prior to collecting nucleus accumbens tissue. The goal of this experiment was to determine the nucleus accumbens transcriptional response specific to separation from an opposite-sex partner. RNA sequencing was done on polyA enriched transcripts using Illumina single-end sequencing. Samples from 3 groups were from a Ribo-seq protocol using a virally delievered, vole optimized Translating Ribosome Affinity Purification construct (Heiman et al., 2008). These samples contain files for both the input fraction and the pulldown fraction (denoted with a _P suffix).
2023-04-17 | GSE192661 | GEO
Project description:Genome wide identification of enhancer regions in the retrosplenial cortex of the prairie vole, Microtus ochrogaster.
| PRJNA297599 | ENA
Project description:We examined the fecal microbiota of female prairie voles. This species is socially and, likely, sexually monogamous, and thus serves as a valuable model in which to examine the interaction between the microbiota-gut-brain axis and social behavior. At present, little is known about the gastrointestinal microbiota of prairie voles; therefore, we performed a first characterization of the fecal microbiota using 16S rRNA gene amplicon sequencing. Semiconductor sequencing technology on an Ion Torrent PGM platform was used to assess the composition of fecal microbiotas from twelve female prairie voles. Following quality filtering, 1,017,756 sequencing reads were classified from phylum to genus level. At the phylum level, Firmicutes, Bacteroidetes, and Saccharibacteria were the predominant taxa, while the Bacteriodales, Erysipelotrichaceae, Ruminococcaceae, and Lachnospiraceae contributed the most dominant microbial groups and genera. Microbial community membership was most similar between vole sibling pairs, but consideration of taxon abundances weakened these associations. The interdependence of host factors such as genetics and behavior with the gastrointestinal microbiota is likely to be particularly pronounced in prairie voles. Our pilot characterization of the prairie vole intestinal microbiota revealed a microbial community composition remarkably consistent with the monogastric alimentary system of these rodents and their diet rich in complex plant carbohydrates. The highly social nature of these animals poses specific challenges to microbiome analyses that nonetheless are valuable for advancing research on the microbiota-gut-brain-behavior axis. Our study provides an important basis for future microbiome research in this emerging model organism for studying social behavior.
| S-EPMC5868765 | biostudies-literature
Project description:Background: The ability to form enduring social bonds is characteristic of human nature and as a result, impairments in social affiliation are central features of severe neuropsychiatric disorders including autism spectrum disorders and schizophrenia. Due to its ability to form long-term pair-bonds, the socially monogamous prairie vole (Microtus ochrogaster) has emerged as an excellent model to study the neurobiology of social attachment. Despite the enduring nature of the bond, however, surprisingly few genes have been implicated in the pair-bonding process in either sex. Results: Using RNA-sequencing, we aimed at identifying the transcriptomic regulations in the nucleus accumbens (NAc) underlying the formation and maintenance of a pair-bond in male and female prairie voles and found sex-specific response patterns despite similar behavioral indicators of pair-bond establishment. Indeed, 24 hrs of cohabitation with an opposite-sex partner induced widespread transcriptomic changes that remained sustained to some extent in females after 3 weeks, but returned to baseline before a second set of regulations in males. This led to a highly sexually-biased NAc transcriptome in the later phase of the bond related to processes such as neurotransmission, protein turnover, and DNA transcription. In particular, we found sex-specific alterations of mitochondrial dynamics following cohabitation, with a shift towards fission in males. Conclusions: In addition to identifying the genes, networks, and pathways involved in the pair-bonding process in the NAc, our work illustrates the vast extent of sex differences in the molecular mechanisms underlying pair-bonding in prairie voles, and paves the way to further our understanding of the complex social bonding process.
2023-04-28 | GSE150080 | GEO
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from several tissues from prairie voles (Microtus ochrogaster). Ear, liver, and brain samples from the Cornell University prairie vole colony were collected from 48 male and female prairie voles at various life stages: neonatal (<1 month old), sub-adult (2-4 months old), mature adult (4-10 months old), and middle aged/old adult (>10 months old). The pair bonded male and female prairie voles used in our study cohabitated with their partners for several months and produced at least three generations of litters. Animals were euthanized via rapid decapitation, their tissues rapidly extracted and frozen on dry ice before being stored at -80C until further processing for genomic DNA extraction. Brains were coronally sectioned and brain regions from the pair bonding circuit (PBC) were micro-dissected and pooled for each animal. The PBC brain regions included the prefrontal cortex, nucleus accumbens, lateral septum, ventral pallidum, and medial amygdala, and ventral tegmental area. Genomic DNA was isolated and purified using the phenol-chloroform extraction and ethanol precipitation method. A total of 144 tissue samples were collected and processed for DNA methylation analysis. Tissues: Brain, Ear, Liver
2023-08-07 | GSE174758 | GEO
Project description:BackgroundRecent research suggests integration of the intestinal microbiota in gut-brain communication which could lead to new approaches to treat neurological disorders. The highly social prairie voles are an excellent model system to study the effects of environmental factors on social behavior. For future studies on the role of probiotics in ameliorating disorders with social withdrawal symptoms, we report the characterization of intestinal Lactobacillus isolates with probiotic potential from voles.Methods and results30 bacterial strains were isolated from the vole intestine and found to be distinct but closely related to Lactobacillus johnsonii using 16S rRNA gene sequencing and Random Amplification of Polymorphic DNA fingerprinting. In vitro characterizations including acid and bile tolerance, antimicrobial effects, antibiotic susceptibility, and adherence to intestinal epithelial cells were performed to assess the probiotic potential of selected strains. Since previous studies revealed that mercury ingestion triggers social deficits in voles, mercury resistance of the probiotic candidates was evaluated which could be an important factor in preventing/treating these behavioral changes.ConclusionsThis study demonstrates that lactobacilli with probiotic potential are present in the vole intestine. The Lactobacillus isolates identified in this study will provide a basis for the investigation of probiotic effects in the vole behavioral model system.
| S-EPMC4696317 | biostudies-literature
Project description:We use ChIP-seq targeting histone 3 lysine 27-acetylation (H3K27ac) to identify putative enhancer sites genome-wide in the ventral pallidum cortex of adult prairie voles
2018-01-31 | GSE85826 | GEO