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
Project description:This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr.
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.
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.
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.
Project description:This dataset contains whole-genome RNA sequencing results from rat embryonic hippocampal neuronal cultures and serves as the basis for characterization of CRISPR/dCas9 gene activation in neuronal systems.
