Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1021276 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: Next-generation sequencing (NGS) technology was used to map expression profile of hippocampal tissue in mouse model of Systemic Lupus Erythematosus (SLE). Methods: Total RNA was extracted from total hippocampal tissue using NucleoSpinRNA and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit. Single-end 100bp mRNA sequencing was performed on Illumina NextSeq500 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package. Results: We defined hippocampal-specific molecular signatures of the murine lupus transcriptome. Conclusions: By the use of the mouse hippocampal-specific transcriptome and through characterization of hippocampal neurogenesis, we showed that inflammatory mediators induce neuropsychiatric changes in SLE as an early event via the disruption of hippocampal neurogenesis. These data underscore the role of brain inflammation in the pathogenesis of early disease and support the use of immunosuppressants for the management of diffuse NPSLE.
2023-05-17 | GSE217939 | GEO
Project description:Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the neuronal CIRT KCNMA1i16 contributes to the firing properties of hippocampal neurons. We hypothesized that CIRTs may be present in a broad set of transcripts and comprise novel signals for post-transcriptional regulation. We carried out a transcriptome-wide survey of CIRTs by sequencing micro-dissected subcellular RNA fractions. Two batches of 150-300 individually dissected dendrites from primary cultures of hippocampal neurons in rat and three batches from mouse hippocampal neurons were sequenced. After statistical processing to minimize artifacts, we found a broad prevalence of CIRTs in the neurons in both species (44-60% of the expressed transcripts). The analysis for CIRTs was also carried out by sequencing single cells from mouse brown adipose tissue and mouse cardiomyocytes. There was widespread prevalence of CIRTs in all of the cell types. Single cell samples were aRNA amplified and sequenced using Illumina GA Analyzer II and Illumina Hiseq 2000
2013-10-15 | E-GEOD-49592 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to compare next-generation sequencing-derived hippocampal transcriptome profiling from mice lacking hippocampal Acetycholine release to evaluate the role of the neurotransmitter in hippocampal gene expression.
2017-12-31 | E-MTAB-3897 | biostudies-arrayexpress
Project description:Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the neuronal CIRT KCNMA1i16 contributes to the firing properties of hippocampal neurons. We hypothesized that CIRTs may be present in a broad set of transcripts and comprise novel signals for post-transcriptional regulation. We carried out a transcriptome-wide survey of CIRTs by sequencing micro-dissected subcellular RNA fractions. Two batches of 150-300 individually dissected dendrites from primary cultures of hippocampal neurons in rat and three batches from mouse hippocampal neurons were sequenced. After statistical processing to minimize artifacts, we found a broad prevalence of CIRTs in the neurons in both species (44-60% of the expressed transcripts). The analysis for CIRTs was also carried out by sequencing single cells from mouse brown adipose tissue and mouse cardiomyocytes. There was widespread prevalence of CIRTs in all of the cell types.
2013-10-15 | GSE49592 | GEO
Project description:We used RNA sequencing of mouse hippocampal tissue two and four weeks after viral-mediated knockdown of SKA2, in order to examine if transcriptional changes might be associated with a hyperactivated secretory autophagy pathway.
2024-02-26 | GSE181203 | GEO
Project description:Mesial temporal lobe epilepsy (mTLE) is a chronic neurological disease characterized by recurrent seizures. The pathogenic mechanisms underlying TLE involve defects in post-transcriptional regulation of gene expression. Previously we have shown the differences in cell compartment specific differential expression of coding transcripts in mTLE hippocampal and cortical samples compared to post-mortem controls (Vangoor et al., MedRxiv. 2021). On the same set of patient samples containing subcellular RNA from resected hippocampal (HC) and neo-cortical (Cx) tissue from mTLE no hippocampal sclerosis (non-HS) and mTLE HS International League Against Epilepsy (ILAE) Type 1 or mTLE+HS patients and postmortem control tissue, we applied small RNA sequencing (smRNA-seq). SmRNA-seq was analyzed for investigating the expression profiles of small non-coding RNA species as microRNAs and transferRNA fragments in human mTLE and control hippocampal tissue.
2024-11-06 | GSE245228 | GEO
Project description:Mesial temporal lobe epilepsy (mTLE) is a chronic neurological disease characterized by recurrent seizures. The pathogenic mechanisms underlying TLE involve defects in post-transcriptional regulation of gene expression. So far, transcriptome profiles from epileptic tissue have been performed using whole cells, thereby lacking information on RNA localization and function at a subcellular level. In this project, we set out to understand the compartment-specific total RNA profile of human mTLE tissue samples. For this, we had established a protocol to isolate cytoplasmic and nuclear compartments from human hippocampal tissue. Subcellular RNA was isolated from resected hippocampal (HC) and neo-cortical (Cx) tissue from mTLE no hippocampal sclerosis (non-HS) and mTLE HS International League Against Epilepsy (ILAE) Type 1 or mTLE+HS patients and postmortem control tissue. Later, we used total RNA sequencing (RNA-seq) to profile for the distinct RNA localization in mTLE in comparison to postmortem control tissue and identified disease related pathways in individual cell compartments. Here we report the total RNAseq (coding and non-coding) data.
2022-03-31 | GSE186334 | GEO
Project description:This experiment was performed to analyze the contribution of NLRP3 inflammasome activation to age-related changes in hippocampal RNA. The hypothesis was that decreased inflammasome activation would reduce hippocampal inflammation. Results indicate that inflammasome knockout animals are protected from age-related changes in hippocampal gene expression Gene expression profiles of young (1 month) and old (21-23 month) wild type, CIAS -/- and ASC -/- mouse hippocampal tissue were compared. Total mRNA was extracted using Trizol.
2013-09-05 | E-GEOD-43034 | biostudies-arrayexpress