Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory.

ABSTRACT: We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: Baf53b+/- homecage (Baf53b+/- HC); Baf53b+/- behavior (Baf53b+/- Beh); wildtype homecage (WT HC); and wildtype behavior (WT Beh). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed thirty minutes following Object Location Memory training. The objective of this study was to examine activity regulated gene expression following a learning event (HC vs Beh) in wildtype and Baf53b+/- mutant mice. Examination of gene expression following a learning event in wildtype and Baf53b+/- mutant mice in dorsal hippocampus.

ORGANISM(S): Mus musculus

SUBMITTER: Annie Vogel-Ciernia

PROVIDER: E-GEOD-44229 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The Neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory.

Project description:We performed an RNA Sequencing experiment on dorsal hippocampal tissue from four groups of animals: Baf53b+/- homecage (Baf53b+/- HC); Baf53b+/- behavior (Baf53b+/- Beh); wildtype homecage (WT HC); and wildtype behavior (WT Beh). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed thirty minutes following Object Location Memory training. The objective of this study was to examine activity regulated gene expression following a learning event (HC vs Beh) in wildtype and Baf53b+/- mutant mice.

2013-03-24 | GSE44229 | GEO

HDAC3-mediated regulation of the circadian gene Per1 contributes to age-related impairments in hippocampal memory and synaptic plasticity

Project description:We performed an RNA Sequencing experiment on dorsal hippocampal tissue from six groups of animals: Aging (18-20-month-old) HDAC3flox/flox homecage (H3F-HC); Aging (18-20-month-old) HDAC3flox/flox 60min post training (H3F-BV); Aging (18-20-month-old) wildtype homecage (OWT-HC); Aging (18-20-month-old) wildtype 60min post training (OWT-BV); Young (2-4-month-old) wildtype homecage (YWT-HC); Young (2-4-month-old) wildtype 60min post training (YWT-BV). Homecage animals were sacrificed directly from the animal's cage. Behavior animals were sacrificed sixty minutes following a 10min Object Location Memory training session.

2018-07-16 | GSE94832 | GEO

LRP8-Reelin-regulated Neuronal (LRN) Enhancer signature underlying learning and memory formation (ChIP-Seq)

Project description:A comprehensive landscape of epigenomic events regulated by the Reelin signaling through activation of specific cohort of cis-regulatory enhancer elements (LRN-enhancers), which involves the proteolytical processing of the LRP8 receptor by the gamma-secretase activity and is required for learning and memory behavior All ChIP-Seq experiments were designed to understand the unique signature and function of LRN-enhancers in signaling pathways of learning and memory.

2015-04-29 | E-GEOD-66701 | biostudies-arrayexpress

Genome-wide maps of chromatin changes uppon contextual fear conditioning in mice (RNA-seq)

Project description:The ability to form memories is a prerequisite for an organismâs behavioural adaptation to environmental changes. At the molecular level, the acquisition and maintenance of memory requires changes in chromatin modifications. In an effort to unravel the epigenetic network underlying both short- and long-term memory, we examined chromatin modification changes in two distinct mouse brain regions, two cell-types, and three time-points before and after contextual learning. Here we show that histone modifications predominantly change during memory acquisition and correlate surprisingly little with changes in gene expression. While long-lasting changes are almost exclusive to neurons, learning-related histone modification and DNA methylation changes occur also in non-neuronal cell types, suggesting a functional role for non-neuronal cells in epigenetic learning. Finally, our data provides evidence for a molecular framework of memory acquisition and maintenance, wherein DNA methylation could alter the expression and splicing of genes involved in functional plasticity and synaptic wiring. We examined chromatin modification changes in two distinct mouse brain regions (CA1 and ACC), two cell-types (neurons, non-neurons), and three time-points before and after contextual learning (naive, 1h, 4w).

2015-11-24 | E-GEOD-74966 | biostudies-arrayexpress

microarray of Amygdala of CTA rats

Project description:Feeding is an important activity for all animals providing nutrients essential for survival and reproduction. Not surprisingly, learning plays a critical role in feeding behavior through the establishment and strengthening of food preferences and aversions. That is, the integration of taste and post ingestive visceral signals in the brain results in memorial representations about the consequences associated with ingesting a particular food. For example, when ingestion of a food is followed by negative gastrointestinal consequences (e.g. nausea, sickness, or vomiting), the animal develops a conditioned taste aversion (CTA), which produces a switch from acceptance to avoidance of that and any like tasting stimulus. Despite recent advances in understanding CTA responsive intracellular signaling pathways in the amygdala, little is known about any long-term regulation of target gene expression following CTA memory consolidation and retrieval. The present study utilized oligo-nucleotide microarray to understand the genes and networks involved in Conditional Taste Aversion Behavior.

2011-02-06 | E-MEXP-3029 | biostudies-arrayexpress

Proteomics on Nav1.8-positive nociceptors of mouse DRG

Project description:Nociceptors play an essential role in both acute pain and chronic pain conditions. In this study, we examined the proteome of mouse dorsal root ganglia and compared NaV1.8Cre+/-; ROSA26-flox-stop-flox-DTA (Diphtheria toxin fragment A) mutant mice (NaV1.8Cre-DTA), in which NaV1.8-positive neurons (mainly nociceptors) in dorsal root ganglia (DRG) were ablated, with respective littermate wildtype controls.

2022-10-03 | PXD034447 | Pride

LTM in CA1 Aged versus young rats

Project description:The aim of this study was to investigate whether the differences in memory decline associated with aging are a result of differences in gene expression. We first categorized age-unimpaired and age-impaired rats based on their performance in the Morris Water Maze and then isolated messenger RNA from the CA1 hippocampal region of each animal to interrogate Affymetrix microarrays. Microarray analysis (p<0.005) identified a set of 50 genes that were transcribed differently in age-unimpaired animals that had successfully learned a spatial task compared to aged learning-impaired animals and a variety of groups designed to control for all non-learning aspects of exposure to the water maze paradigm. Keywords: behavior comparison, age comparison

2006-06-30 | GSE3531 | GEO

Genome-wide maps of chromatin changes uppon contextual fear conditioning in mice (meDIP-seq)

2015-11-24 | E-GEOD-74965 | biostudies-arrayexpress

Cellular Resiliency and Survival of a Neuro-2a Cell Line Under Extreme Stress

Project description:Stressors such as hypoxia, hypothermia, and acute toxicity often result in widespread cell death. Recently, the failure of a cryostorage dewar in our lab resulted in prolonged thawing of Neuro-2a cells, exposing them to a combination of these insults. Surprisingly, a small fraction of the cells survived the event, underwent a period of near-dormancy, and were able to fully recover to a healthy state. To investigate this unusual resiliency, we established a novel standardized model to recapitulate the event and charted the phenotypes, transcriptomes, proteomes, and mitochondrial dynamics of the surviving cells along the trajectory of recovery. We observed an enrichment in DNA-repair and chromatin modification pathways bolstered by highly elevated mitochondrial activity in the immediate aftermath of the event and through the early stages of recovery, with subsequent normalization toward that of controls as the cells completed their recovery. Our results indicate that a robust energetic state that helps sustain DNA repair and stress-responsive pathways at the earliest stages of recovery facilitate cell survival and resiliency following extreme stress.

2024-11-26 | PXD053015 | Pride

A Cell Type-Specific Approach to Elucidate the Role of miR-96 in Inner Ear Hair Cells

Project description:Mutations in miRNA-96, a microRNA expressed within the hair cells (HCs) of the inner ear, result in progressive hearing loss in both mouse models and humans. While previous studies have delved into miR-96 transcriptional cascades via whole organ of Corti microarray experiments of diminuendo (Mir96Dmdo) mice, they face limitations in pinpointing cell type-specific differentially expressed genes. This hinders the ability to conclusively determine if the effects of Mir96Dmdo are specifically within HCs and contribute to the observed abnormal Mir96Dmdo HC phenotype and determine the role of miR-96 in HCs. In this study, we generate the first HC-specific RNA-sequencing (RNA-seq) datasets from Mir96Dmdo; Atoh1/nGFP+ postnatal day 1 wildtype, heterozygous, and homozygous mutant mice. Our differential gene expression analysis between Mir96Dmdo homozygous mutant HCs compared to wildtype HCs identified 215 upregulated and 428 downregulated genes. Many significantly downregulated genes in Mir96Dmdo homozygous mutant HCs have established roles in HC development and/or known roles in deafness such as Myo15, Myo7a, Ush1c Gfi1, and Ptprq, some of which were not previously identified in other miR-96 datasets. In addition, active modules of protein-protein interaction networks of significantly downregulated genes in Mir96Dmdo homozygous mutant HCs reveal enrichment in GO terms with biological functions such as sound perception and endocytosis. Genes significantly upregulated in Mir96Dmdo homozygous mutant HCs, which are more likely to be direct targets of miR-96, show higher expression in wildtype supporting cells compared to wildtype HCs, suggesting a role of miR-96 in suppressing non-HC genes during HC development. Finally, all generated HC-specific Mir96Dmdo RNA-seq datasets from this manuscript are now publicly available in the miR-96 specific gEAR profile (https://umgear.org/p?l=miR96).

2024-05-09 | GSE255796 | 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