Circular RNA circRERE2 knockdown in rat primary cortical neurons
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ABSTRACT:
PROVIDER: PRJNA1088105 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Circular RNA circRERE2 knockdown in rat primary cortical neurons [miRNA-seq]
| PRJNA1088107 | ENA
Project description:Circular RNA circRERE2 knockdown in rat primary cortical neurons [polyA RNA-seq]
| PRJNA1088101 | ENA
Project description:E18 embryonic rat cortical neurons cultured in vitro are infected with lentivirus expressing control or PHF6shRNA-2, and harvested 5 days after infection pLL3.7 lentivirus expressing control or PHF6shRNA-2 was generated in 293T cells and concentrated using ultracentrifuge. In vitro cultured cortical neurons were infected and RNA was harvested 5 days after infection. PHF6 knockdown was validated by QPCR before sample was processed for microarray analysis.
2013-08-01 | E-GEOD-45953 | biostudies-arrayexpress
Project description:Circular RNAs (circRNAs), a diverse class of ncRNAs highly enriched in developing neurons, play roles in local protein synthesis and synaptic plasticity. However, distinguishing functional from non-functional circRNAs is challenged by their abundance, tissue specificity and splicing variability. To address this, we conducted a RNAi knockdown screen targeting 32 highly expressed, conserved circRNAs enriched in dendritic processes. circRERE isoforms emerged as regulators of dendritic synapse density and electrophysiological characteristics. mRNA-seq supports the dysregulation of synaptic genes, particularly miR-128-3p-sensitive transcripts. MiR-128-3p activity and expression are reduced, with circRERE possessing multiple miR-128-3p binding sites, suggesting a protective interaction supported by a rescue of the synaptic phenotype upon miR-128-3p overexpression. Conversely, circRERE overexpression with intact miR-128-3p sites rescued the synaptic phenotype and independently increased miR-128-3p levels. These findings demonstrate the necessity for the broad characterization of circRNAs in the nervous system to comprehensively understand their influence on essential non-coding RNA regulatory networks.
2024-03-18 | GSE261609 | GEO
Project description:Circular RNAs (circRNAs), a diverse class of ncRNAs highly enriched in developing neurons, play roles in local protein synthesis and synaptic plasticity. However, distinguishing functional from non-functional circRNAs is challenged by their abundance, tissue specificity and splicing variability. To address this, we conducted a RNAi knockdown screen targeting 32 highly expressed, conserved circRNAs enriched in dendritic processes. circRERE isoforms emerged as regulators of dendritic synapse density and electrophysiological characteristics. mRNA-seq supports the dysregulation of synaptic genes, particularly miR-128-3p-sensitive transcripts. MiR-128-3p activity and expression are reduced, with circRERE possessing multiple miR-128-3p binding sites, suggesting a protective interaction supported by a rescue of the synaptic phenotype upon miR-128-3p overexpression. Conversely, circRERE overexpression with intact miR-128-3p sites rescued the synaptic phenotype and independently increased miR-128-3p levels. These findings demonstrate the necessity for the broad characterization of circRNAs in the nervous system to comprehensively understand their influence on essential non-coding RNA regulatory networks.
2024-03-18 | GSE261607 | GEO
Project description:E18 embryonic rat cortical neurons cultured in vitro are infected with lentivirus expressing control or PHF6shRNA-2, and harvested 5 days after infection
2013-08-01 | GSE45953 | GEO
Project description:Inhaled anesthetics produce many effects and bind to a large number of brain proteins, but it is not yet clear if this is accompanied by widespread changes in gene expression of the biological targets. Such changes in expression might implicate functionally important targets from the large pool of binding targets. Isolated primary cortical neurons were exposed to anesthetics and DNA oligonucleotide microarrays were used to detect and quantify transcriptional changes in neuronal tissue. Experiment Overall Design: Primary cortical neurons were treated with 1MAC, 3MAC Halothane and 3MAC Isoflurane, together with no drug control. Pool no drug control was used as Cy3 channel in all chips. The above drug treated and individual control samples were used in Cy5 channel.
2008-05-07 | E-GEOD-2982 | biostudies-arrayexpress
Project description:RNA Binding Motif 5 (RBM5) is a nuclear splicing factor. Prior studies show that RBM5 overexpression in cancer cells alters gene splicing, gene expression, and induces cell death and/or growth arrest. The role of RBM5 in primary neurons is unknown, and its potential mRNA targets have not been identified. Using lentivirus based approaches we tested if RBM5 knockdown (i.e. by shRNA) or RBM5 overexpression (DDK-tagged rat open reading frame) alters whole genome expression in primary rat cortical neurons. We used microarrays to examine genes that are up-regulated vs. down-regulation in cortical neurons after RBM5 knockdown vs. overexpression.
2018-02-16 | GSE98858 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-03-18 | GSE261610 | GEO
Project description:For identification of transcripts enriched in neurites of primary cortical neurons, the cells were plated on a microporous membrane for isolation of neurites and soma. Extracted RNA was used for preparation of mRNA-seq, total RNA-seq or smRNA-seq libraries and Illumina sequencing. For neuronal zipcode identification protocol (N-zip) in mouse cortical neurons, we combined a massively parallel reporter assay with neurites/soma separation. Neurons, grown on a microporous membrane, were infected with a library of around 5000 oligos tiled across 3'UTRs of selected neurite-enriched transcripts, cloned downstream of GFP coding sequence. RNA was extracted from soma and neurites and reverse transcribed into cDNA. Amplicon libraries of 3'UTR reporters were prepared and subjected to Illumina sequencing. In the second round of N-zip, a library containing selected reporters from the first N-zip and their mutagenized versions (around 6000 oligos) were used. In the following rounds, N-zip was combined with knockdown of selected genes.
2022-12-02 | E-MTAB-10902 | biostudies-arrayexpress