Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional differentiation along the longitudinal axis of the developing hippocampus.

ABSTRACT: The role of the hippocampus in learning and memory has been widely studied. However, studies of differences along the longitudinal axis indicate that the hippocampus is perhaps not a singular structure, but instead it is thought that the dorsal and ventral poles of the hippocampus have functional differences. An anatomical gradient of hippocampal inputs along the dorsal-ventral axis supports this notion. It has been recently shown that there is transcriptional differentiation along the longitudinal axis of the adult hippocampus, coinciding with functional and anatomical gradients. Understanding the development of the dorsal-ventral hippocampal axis will further our understanding of the different hippocmapal functional contributions along the longitudinal axis. However, analysis of transcriptional gradients along the dorsal ventral axis have not been studied in the neonatal rat during development. We performed an extensive bead-chip based geneome-wide analysis of transcriptional differences in dorsal, intermediate, and ventral hippocampal tissue of rats aged postnatal day 0 (P0), P9, P18 and P60.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Arnar Flatberg

PROVIDER: E-MTAB-2617 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Distinct transcriptomic, proteomic and epigenetic stress-responses in dorsal and ventral hippocampus

Project description:The hippocampus - one of the most studied brain regions – is a key target of the stress response and vulnerable to the detrimental effects of stress. Although its intrinsic organization is highly conserved throughout its long dorsal-ventral axis, the dorsal hippocampus is linked to spatial navigation and memory formation, whereas the ventral hippocampus is linked to emotional regulation. Here, we provide the first combined transcriptomic and proteomic profiling that reveals striking differences between dorsal and ventral hippocampus. Using various acute stress challenges we demonstrate that both regions display very distinct molecular responses, and that the ventral hippocampus is particularly responsive to the effects of stress. We demonstrate that separately analyzing dorsal and ventral hippocampus greatly increases the ability to detect region-specific stress effects, and we identify an epigenetic network, which is specifically sensitive to acute stress in the ventral hippocampus.

2019-10-03 | PXD006781 | Pride

Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans

Project description:The hippocampus supports many facets of cognition, including learning, memory, and emotional processing. Anatomically, the hippocampus runs along a longitudinal axis, posterior-to-anterior in primates (corresponding to dorsal-to-ventral in rodents). The structure, function, and connectivity of the hippocampus vary along this axis. In rodents, experiments have established the cellular, molecular, and functional heterogeneity along the hippocampal axis, resulting in comprehensive models of specialization that integrate these different types of information. In humans however, functional heterogeneity remains an active area of investigation, and structural heterogeneity has not been described. To better understand the cellular composition and molecular diversity along the hippocampal long axis in the human brain and define distinct molecular signatures corresponding to functional domains we performed single-nuclei RNA-sequencing on surgically resected human anterior and posterior hippocampus. Analysis of 131,325 nuclei revealed differentially expressed genes between the anterior and posterior human hippocampus at cellular resolution. We determine the program of these axis- and cell-type specific genes that are conserved in the mouse hippocampus, and we also identify patterns that are differential between the human and mouse. We further identify axis- and cell-type specific gene expression signatures that differentially intersect with human cognitive and neuropsychiatric genetic signals, identifying cell type-specific genes in the posterior hippocampus for cognitive function and in the anterior hippocampus for mood and affect. Our data illuminate a region- and cell-type-specific transcriptional landscape within the hippocampus. This data is accessible as a public resource through an interactive website (https://human-hippo-axis.cells.ucsc.edu/) and will act as a reference atlas for the human hippocampus.

2021-05-03 | GSE160189 | GEO

Detailed analysis of dorsal-ventral gradients of gene expression in the rat hippocampus

Project description:Dorsal and ventral parts of the hippocampus despite similar histological structure are known to be involved in performance of different functions. Previous studies using next generation sequencing showed that these two hippocampal parts differ in the expression of many genes, however, stability of dorsoventral gradient of gene expression remains open question. Here, we analyzed differential expression of genes between the dorsal and ventral hippocampus of rats in polyA-enriched samples and samples subjected to depletion of ribosomal RNA. We present here a detailed analysis of differentially expressed genes between the dorsal and ventral parts of the hippocampus. Intersection of our dataset with data of previous RNAseq studies revealed 544 genes are stably differentially expressed between the hippocampal parts suggesting that, despite strongly variability between the animals and sequencing approaches, there is a subset of genes whose expression stably differs between the dorsal and ventral hippocampus. Analysis of differential splicing showed that the dorsal and ventral parts of the hippocampus express 64 genes whose splice isoforms are different between the hippocampal parts. Furthermore, we show that depletion of ribosomal RNA increases representation of transposable elements in the RNAseq libraries and helps to detect a weak predominance of expression of these elements in the ventral hippocampus.

2022-07-19 | GSE208330 | GEO

Floc'hlay2020 - SeaUrchin_model_ginsim

Project description:Multilevel logical model encompassing the Nodal and BMP pathways together with key transcription factors setting the dorsal-ventral axis in the sea urchin P. lividus embryo. This model accounts for the specification of wild-type ventral ectoderm, ciliary band and dorsal ectoderm, and further recapitulates sophisticated mutant phenotypes.

2021-01-06 | MODEL2002190001 | BioModels

Micro-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Micro-C was carried out for control embryos and embryos produced from gd7 mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis (dorsal ectoderm). We used these embryos to compare chromatin conformation across tissues.

2021-01-08 | E-MTAB-9784 | biostudies-arrayexpress

Proteomic profile of hippocampus regions from the pilocarpine medial temporal lobe epilepsy model

Project description:Label-free Proteomic profile of the dentate gyrus (dorsal and ventral) and CA3 (dorsal and ventral) microdissected from the hippocampus of the pilocarpine model of Mesial Temporal Lobe Epilepsy.

2024-03-25 | MSV000094401 | MassIVE

Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice

Project description:TET3 is a member of the Ten-eleven translocation (TET) family of enzymes which oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Tet3 is highly expressed in the brain, where 5hmC levels are most abundant. In adult mice, we observed that TET3 is present in mature neurons and oligodendrocytes but is absent in astrocytes. To investigate the function of TET3 in adult post-mitotic neurons, we crossed Tet3 floxed mice with a neuronal Cre-expressing mouse line, Camk2a-CreERT2, obtaining a Tet3 conditional KO mouse line. Ablation of Tet3 in adult mature neurons resulted in increased anxiety-like behavior with concomitant hypercorticalism, and impaired hippocampal-dependent spatial orientation. Transcriptome and gene-specific expression analysis of the hippocampus showed dysregulation of genes involved in glucocorticoid signaling pathway (HPA axis) in the ventral hippocampus, whereas upregulation of immediate early genes (IEGs) was observed in both dorsal and ventral hippocampal areas. Additionally, Tet3 cKO mice exhibit increased dendritic spine maturation in the ventral CA1 hippocampal subregion. Based on these observations, we suggest that TET3 is involved in molecular alterations, that govern hippocampal-dependent functions. These results reveal a critical role for epigenetic modifications in modulating brain functions, opening new insights into the molecular basis of psychiatric disorders.

2020-01-16 | GSE140850 | GEO

ChIP-seq of Drosophila embryos to investigate chromatin state during dorsal-ventral patterning

Project description:We carried out ChIP-seq for H3K27ac and H3K27me3 in embryos from Tollrm9/rm10 mutant mothers. The embryos from mutant mothers produce only a single tissue type (neuroectoderm) along the dorsal-ventral axis. We used these embryos to compare chromatin state across tissues.

2021-01-08 | E-MTAB-9303 | biostudies-arrayexpress

Hi-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Hi-C was carried out for control embryos and embryos produced from gd7, Tollrm9/rm10, and Toll10B mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis. We used these embryos to compare chromatin conformation across tissues.

2021-01-08 | E-MTAB-9306 | biostudies-arrayexpress

RNA sequencing of whole, ventral and dorsal hippocampus after different stress conditions

Project description:Purpose: The goal of this study was to characterize molecular stress responses on transcriptional level in dorsal and ventral hippocampus separately. Methods: mRNA profiles of whole, dorsal and ventral hippocampus of mice 45min after first exposure to different acute stressors. The stressors were novelty (6min novel environment), restraint (30min immobilization), or cold swim (6min in 18 degree Celcius water). 5 mice were used per condition, using Illumina HiSeq4000. The sequence reads that passed quality filters were mapped with STAR, counted with RSEM and differential gene expression was calculated using the bioconducter package edgeR. Results: With our workflow, we identified 13902 genes per sample. Approximately 20% of the genes were differentially expressed between dorsal and ventral hippocampus at baseline, with a log2 fold change >±0.3 and p value <0.005. Approximately 100 genes are differentially expressed upon stress treatment in the whole hippocampus. If ventral and dorsal hippocampus were analyzed separately, numbers increased to 150 and 250 respectively. Stress-responsive genes vary between dorsal and ventral hippocampus, and also vary between different stressors. Further analysis identified a functional epigenetic gene cluster specific for the stress response in the ventral hippocampus. Conclusions: Our study represents the first RNA-seq analysis of dorsal and ventral hippocampus after different acute stress exposures.

2018-02-08 | GSE100236 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data