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RNA Sequencing quantitatively profiles chemical long-term potentiation (LTP) induced gene transcription alteration

ABSTRACT: RNA Sequencing quantitatively profiles chemical long-term potentiation (LTP) induced gene transcription alteration

PROVIDER: PRJNA434759 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6756850.fastq.gz	Fastqsanger.gz
	SRR6756851.fastq.gz	Fastqsanger.gz
	SRR6756852.fastq.gz	Fastqsanger.gz
	SRR6756853.fastq.gz	Fastqsanger.gz
	SRR6756854.fastq.gz	Fastqsanger.gz

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RNA Sequencing quantitatively profiles chemical long-term potentiation (LTP) induced gene transcription alteration

Project description:To identify proteins involved in activity dependent synaptic remodeling that are not caused by changes in mRNA levels we performed RNA-seq and TMT-based quantitative MS.

2021-02-20 | GSE110908 | GEO

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP) [RNA-Seq]

Project description:This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during long-term potentiation (LTP) of mouse hippocampal CA3-CA1 synapses. Transcriptome analysis allowed to identify changes in gene expression and alternative splicing induced 1 hour and 3 hours after LTP induction.

2018-02-22 | GSE84503 | GEO

DNA-methylation of LTP-associated genes.

Project description:Long-term potentiation (LTP) of synaptic transmission is recognized as a cellular mechanism for learning and memory storage. Although de novo gene transcription is known to be required in the formation of stable LTP, the molecular mechanisms underlying synaptic plasticity remain elusive.This study investigates the DNA-methylation levels of promoters and CpG-islands of LTP-associated genes identified from Maag et al. 2015 (DOI: 10.3389/fnins.2015.00351) (See E-MTAB-3375).

2017-03-16 | E-MTAB-4919 | biostudies-arrayexpress

Development of a platform to investigate long term potentiation in human iPSC-derived neuronal networks

Project description:Although impairment of long-term potentiation (LTP) is a common feature of many neurological disorders, studies in humans are limited by inaccessibility of the brain. Human induced pluripotent stem cells (hiPSC) provide a unique opportunity to study LTP, especially in disease specific genetic backgrounds. We describe a multi-electrode array (MEA)-based assay to investigate chemically induced LTP (cLTP) in networks of hiPSC-derived midbrain dopaminergic (DA) and cortical neuronal populations. We demonstrate potentiation of activity that lasts for days, allowing for studies of the late phases of LTP. We show that cLTP on midbrain DA neuronal networks is largely independent of the N-methyl-D-aspartate receptor (NMDAR), and demonstrate partial dependence on brain derived neurotrophic factor (BDNF), as well as other factors released into the medium. Finally, we describe activity-regulated gene expression induced by cLTP. In summary, this cLTP-MEA assay platform will enable phenotype discovery and higher throughput analyses of synaptic plasticity on hiPSC-derived neurons.

2022-08-18 | GSE193191 | GEO

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)

Project description:Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) During Hippocampal Long-Term Potentiation (LTP)

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Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation (APA) during hippocampal Long-Term Potentiation (LTP) [3'READS]

Project description:This study was aimed at elucidating the mechanisms underlying activity-dependent gene regulation during LTP of mouse hippocampal CA3-CA1 synapses. Deep sequencing of the 3’ end of transcripts allowed to identify changes in APA induced 1 hour and 3 hours after LTP induction. We detected APA changes that only affected the 3'UTR (3'UTR-APA events) and APA changes that also affected the coding sequence (CDS-APA events).

2018-02-22 | GSE84643 | GEO

Mapping Gene Expression in Excitatory Neurons During Hippocampal Late-Phase Long-term Potentiation

Project description:The long-lasting changes in synaptic connectivity that underlie long-term memory require new RNA and protein synthesis for their persistence. To elucidate the temporal pattern of gene expression that gives rise to long-lasting, learning-related neuronal plasticity, we profiled RNAs in mouse hippocampal CA3-CA1 slices following induction of late phase long-term potentiation (LTP), analyzing differential expression (DE) specifically within pyramidal excitatory neurons by Translating Ribosome Affinity Purification RNA sequencing (TRAP-seq). We detected time-dependent changes in up- and down-regulated ribosome-associated mRNAs over the two hours following LTP induction, with minimal overlap of DE transcripts between time points. TRAP-seq revealed greater numbers and amplitudes of LTP-induced changes than RNA-seq of all cell types in the hippocampus. Transcripts that were DE by TRAP-seq but not RNA-seq were enriched in mRNAs encoding cytoskeletal and cell adhesion proteins, while RNA-seq identified DE in many non-neuronal mRNAs. Together our results highlight the importance of considering both the time course and the cell-type specificity of activity-dependent gene expression during memory formation.

2017-02-23 | GSE79790 | GEO

The ability of VSL#3 to restore the age-related deficit in LTP is associated with changes in brain genes expression

Project description:A deficit in synaptic plasticity is one of the many changes that occurs with age. Specifically the archetypal model of plasticity, long-term potentiation (LTP), is reduced in hippocampus of middle-aged and aged animals. Several factors are likely to contribute to this deficit including morphological changes like a net loss of neurons and loss of synapses with the consequent changes in receptor signalling. However it is also clear that ageing is associated with development of oxidative stress, and also inflammatory stress which is typified by increased activation of microglia. Recent evidence has indicated that probiotics exert anti-inflammatory in the gut. Specifically VSL#3, a proprietary probiotic comprising 8 Gram-positive bacterial strains, decreased markers of inflammation in the colon in an animal model of colitis. We considered that its anti-inflammatory effects might extend to brain and therefore that treatment of aged rats with VSL#3 might attenuate the age-related deficit in LTP. The evidence indicates that LTP was impaired in control-treated aged rats but sustained in aged rats which received VSL#3. This was accompanied by a modest decrease in markers of microglial activation and an increase in BDNF and synapsin . The microarray analysis demonstrated that VSL#3 treatment induces changes also in the expression of some brain genes. four sample groups each representing a certain treatment condition of young or adult male Han Wistar rats

2014-04-02 | E-GEOD-51381 | biostudies-arrayexpress

Ketogenic diet and BHB rescue the fall of long-term potentiation in an Alzheimer's mouse model and stimulates synaptic plasticity pathway enzymes

Project description:The Ketogenic Diet (KD) improves memory and longevity in aged C57BL/6 mice. We tested 7 months KD vs. control diet (CD) in the mouse Alzheimer's Disease (AD) model APP/PS1. KD significantly rescued Long-Term-Potentiation (LTP) to wild-type levels, not by changing Amyloid-β (Aβ) levels. KD's 'main actor' is thought to be Beta-Hydroxy-butyrate (BHB) whose levels rose significantly in KD vs. CD mice, and BHB itself significantly rescued LTP in APP/PS1 hippocampi. KD's 6 most significant pathways induced in brains by RNAseq all related to Synaptic Plasticity. KD induced significant increases in synaptic plasticity enzymes p-ERK and p-CREB in both sexes, and of brain-derived neurotrophic factor (BDNF) in APP/PS1 females. We suggest KD rescues LTP through BHB's enhancement of synaptic plasticity. LTP falls in Mild-Cognitive Impairment (MCI) of human AD. KD and BHB, because they are an approved diet and supplement respectively, may be most therapeutically and translationally relevant to the MCI phase of Alzheimer's Disease.

2023-12-31 | GSE230469 | GEO

mRNA sequencing analysis of transcripts from CA1 regions 90 minutes after Long-Term Potentiation was induced

Project description:Purpose: Study the differentially expressed genes in hippocampal rat CA1 regions 90 minutes after Long-Term Potentiation (LTP) was induced using field recordings Methods: hippocampal rat CA1 region mRNA profiles of control (unstimulated) and 90 minutes after LTPwas induced (LTP 90) were generated by deep sequencing. A pool of approximately 10 CA1 regions collected from at least 3 different animals were used. The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0 were used. The rn5-bowtie2 index was generated with the command 'bowtie2-build rn5.fa rn5'. The 'rn5.fa'-file was downloaded from the UCSC genome browser. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml. RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files. Conclusions: Our study illustrates the nature of the different transcripts in acute rat hippocampal slices after LTP 90 minutes was induced using field electrophysiology and compares them with control, unstimulated slices. Thius allowed us to identify wich genes are modulated in the hippocampus in order to promote and sustain LTP.

2018-10-02 | GSE120712 | GEO

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