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MiRNA expression profiles of frontal cortex and hippocampus from adult C57BL/6J mice

ABSTRACT: We used Affymetrix miRNA arrays to analyze the expression of miRNAs in the frontal cortex and hippocampus of 8-week-old C57BL/6J wt mice. We compared these microarray-based expression profiles to ones obtained by miRNA sequencing from the same brain regions of the same mouse strain.

ORGANISM(S): Mus musculus synthetic construct

PROVIDER: GSE27891 | GEO | 2011/06/22

SECONDARY ACCESSION(S): PRJNA138195

REPOSITORIES: GEO

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miRNA expression profiles of frontal cortex and hippocampus from adult C57BL/6J mice

Project description:We used Affymetrix miRNA arrays to analyze the expression of miRNAs in the frontal cortex and hippocampus of 8-week-old C57BL/6J wt mice. We compared these microarray-based expression profiles to ones obtained by miRNA sequencing from the same brain regions of the same mouse strain. miRNA expression profiling of frontal cortex and hippocampus from C57BL/6J mice (N=3) was performed with Affymetrix miRNA array

2011-06-22 | E-GEOD-27891 | biostudies-arrayexpress

MiRNA expression profiles from adult mouse frontal cortex and hippocampus

Project description:MicroRNAs (miRNAs) are small regulatory molecules that cause post-transcriptional gene silencing. Although some miRNAs are known to have region-specific expression patterns in the adult brain, the functional consequences of the region-specificity to the gene regulatory networks of the brain nuclei are not clear. Therefore, we studied miRNA expression patterns by miRNA-seq in two brain regions, frontal cortex (FCx) and hippocampus (HP), which have separate biological functions. We identified 354 miRNA from FCx and 408 from HP. Several miRNA families and clusters were differentially expressed between FCx and HP, including the miR-8 family, miR-182|miR-96|miR-183 cluster, and miR-212|miR-312 cluster overexpressed in FCx and miR-34 family overexpressed in HP. To visualize the clusters, we developed support for viewing genomic alignments of miRNA-seq reads in the Chipster genome browser. We carried out pathway analysis of the predicted target genes of differentially expressed miRNA families and clusters to assess their putative biological functions. Interestingly, specific pathways were identified that are predicted to be regulated by several miRNAs from the same family/cluster. We have developed a miRNA-seq approach with a bioinformatic analysis workflow that is suitable for studying miRNA expression patterns from specific brain nuclei. FCx and HP were shown to have distinct miRNA expression patterns which were reflected in the predicted gene regulatory pathways. This methodology can be applied for the identification of brain region-specific and phenotype-specific miRNA-mRNA-regulatory networks from the adult and developing rodent brain. miRNA-seq of 3 replicates from frontal cortex, 3 replicates from hippocampus, and pooled sequence runs from both

2011-06-21 | E-GEOD-27979 | biostudies-arrayexpress

microRNA-sequencing of inbred mouse strain hippocampus and frontal cortex

Project description:Purpose: We carried out small RNA sequencing to determine miRNA expression patterns of hippocampus and frontal cortex in six inbred mouse strains. We analyzed miRNA expression levels, isomiR distribution and miRNA editing events. Methods: We constructed small RNA libraries starting from the total RNA extracted from the hippocampus and frontal cortex of three animals per strain. The sequencing was carried out using Illumina HiSeq2000 (single-end). The sequence reads that passed quality filters were mapped to the mouse genome (mm10) and to known miRNAs (miRBase v21) using miRDeep2, SeqBuster, and sRNAbench, to obtain miRNA and isomiR expression levels and to predict novel miRNAs. Genome alignments were analysed for miRNA editing using FreeBayes. Results: We detected significant miRNA and isomiR expression level differences between the strains and brain regions. Most of the miRNA loci produced a number of isomiRs. Some miRNAs were consistently edited with a pattern that matches the activity of known RNA editing enzymes.

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MiRNA expression profiles from adult mouse frontal cortex and hippocampus

2011-06-22 | GSE27979 | GEO

Ambient RNA analysis of single-nuclei RNA-Seq data from the frontal cortex of C57BL/6J mice

Project description:Contamination of ambient RNA was found in single-nuclei RNA-Seq data of mouse frontal cortex. CellBender plus subcluster cleaning selectively removed ambient RNA signature from glial cell types.

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Ambient RNA analysis of single-nuclei RNA-Seq data from the frontal cortex of C57BL/6J mice

Project description:Ambient RNA analysis of single-nuclei RNA-Seq data from the frontal cortex of C57BL/6J mice

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Small intestinal epithelial cells from C57Bl/6J mice

Project description:Total proteome from sorted primary intestinal epithelial cells isolated from the small intestines of 4 C57Bl/6J mice

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polyA mRNA RNA-seq from frontal cortex (ENCSR000BZS)

Project description:The libraries contained in this experiment come from adult 8 week frontal cortex tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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5-HT4 receptor agonists increase sAPPalpha levels in the cortex and hippocampus of male C57BL/6j mice.

Project description:BACKGROUND AND PURPOSE: A strategy to treat Alzheimer's disease (AD) is to increase the soluble form of amyloid precursor protein (sAPPalpha), a promnesic protein, in the brain. Because strong evidence supports beneficial effects of 5-hydroxytryptamine 5-HT(4) receptor agonists in memory and learning, we investigated the role of 5-HT(4) receptors on APP processing in 8 weeks-old male C57BL/6j mice. EXPERIMENTAL APPROACH: Mice were given, subcutaneously, prucalopride or ML 10302 (s.c.), two highly selective 5-HT(4) receptor agonists and, up to 240 min later, the hippocampus and cortex were analysed by Western blot for sAPPalpha determination. KEY RESULTS: Prucalopride (5 or 10 mg kg(-1)) significantly increased sAPPalpha levels in the hippocampus and cortex, but did not modify the expression level of APP mRNA as detected by quantitative RT-PCR. A selective 5-HT(4) receptor antagonist, GR125487 (1 mg kg(-1), s.c.) inhibited prucalopride induced- increase in sAPPalpha levels. In addition, levels of sAPPalpha were increased by ML10302 only at 20 mg kg(-1) and was limited to the cortex. Also, prucalopride increased sAPPalpha levels in the cortex of a transgenic mouse model of AD, expressing the London mutation of APP. Furthermore, the combined injection of a selective acetylcholinesterase inhibitor, donepezil and prucalopride induced a synergic increase in sAPPalpha levels in the cortex and hippocampus. CONCLUSIONS AND IMPLICATIONS: Our results demonstrate that the 5-HT(4) receptor plays a key role in the non-amyloidogenic pathway of APP metabolism in vivo and give support to the beneficial use of 5-HT(4) agonists for AD treatment.

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Parkinson Disease Frontal Cortex ncRNA Profiling

Project description:Parkinson Disease Frontal Cortex ncRNA Profiling

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