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272 results for “RNA editing”
Alterations in RNA editing in skeletal muscle following exercise training in individuals with Parkinson's disease
<p>Parkinson’s Disease (PD) is the second most common neurodegenerative disease behind Alzheimer’s Disease, currently affecting more than 10 million people worldwide. The progression of PD results in the loss of function due to neurodegeneration and neuroinflammation. The etiology of PD is multifactorial, including both genetic and environmental origins. We explored changes in RNA editing, specifically editing through the actions of the Adenosine Deaminases Acting on RNA (ADARs), in the progression of PD. Analysis of ADAR editing of skeletal muscle transcriptomes from PD patients and controls, including those that engaged in a rehabilitative exercise training program revealed significant differences in ADAR editing patterns based on age, disease status, and following rehabilitative exercise. Further, deleterious editing events in protein coding regions were identified in multiple genes with known associations to PD pathogenesis. Our findings of differential ADAR editing complement findings of changes in transcriptional network identified by a recent Lavin et al. 2020 (<a href="https://doi.org/10.3389/fphys.2020.00653">https://doi.org/10.3389/fphys.2020.00653)</a> study and offer insights into dynamic ADAR editing changes associated with PD pathogenesis. VCF files were generated using AIDD (Plonski et al., 2020) (<a href="https://doi.org/10.1186/s12859-020-03888-6">https://doi.org/10.1186/s12859-020-03888-6</a>).</p>
Double-stranded RNA structural elements holding the key to translational regulation in cancer: the case of editing in RNA Binding Motif Protein 8A
<p>Raw data supporting the manuscript</p> <p>Abukar, A.;Wipplinger, M.;<br> Hariharan, A.; Sun, S.; Ronner, M.;<br> Sculco, M.; Okonska, A.;<br> Kresoja-Rakic, J.; Rehrauer, H.; Qi, W.;<br> et al. Double-Stranded RNA<br> Structural Elements Holding the Key<br> to Translational Regulation in Cancer:<br> The Case of Editing in RNA-Binding<br> Motif Protein 8A. Cells 2021, 10, 3543.<br> https://doi.org/10.3390/<br> cells10123543</p>
Sequencing data of RNA editing, RNA modifications, and transcriptional units in Listeria monocytogenes
<p>Sequencing data for "RNA editing, RNA modifications, and transcriptional units in <em>Listeria monocytogenes</em>" manuscript, which is submitted to BMC genomics.</p>
A data repository for the study of Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
<p><span>This repository contains data associated with the study:</span></p> <p><span><strong>"Alpha-synuclein Aggregates Trigger Anti-Viral Immune Pathways and RNA Editing in Human Astrocytes"</strong></span></p> <p><span>Published as a <strong>bioRxiv preprint</strong>: <a href="https://doi.org/10.1101/2024.02.26.582055"><span>DOI: 10.1101/2024.02.26.582055</span></a></span></p>
Additional data repository for the study of Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes
<p>Zip file 1: astrocytes calcium data measured using Fura 2</p> <p>Zip file2: astrocytes ROS measured using DHE (Dihydroethidium)</p> <p>Zip file 3: astrocytes cell death measured using Sytox green</p>
Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment
<p>Raw data supporting the manuscript</p>
Massive RNA editing in ascetosporean mitochondria
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The expansion and diversification of pentatricopeptide repeat RNA editing factors in plants
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Summary statistics data for "Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes"
<p>edQTL and ASED summary statistics data for the manuscript titled "Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes"</p>
Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes
<p>Premise</p> <p>Recent advances in studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns.</p> <p>Methods</p> <p>We determined plastid RNA editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read mapping and SNP calling software to identify RNA editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene.</p> <p>Results</p> <p>We found direct evidence for 505 and 509 plastid RNA editing sites in A. aleuticum and A. shastense, respectively, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved.</p> <p>Conclusions</p> <p>Variation in RNA editing frequency observed within Adiantum implies that RNA editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.</p>
Supplementary file of A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs
<p><span>Figure S1: PCA analysis of all tissues. Figure S2: wild(CFLAR-A) and experimental(CFLAR-G) plasmid by PCR and Sanger sequencing. Figure S3: Validation of RNA editing by PCR and Sanger sequencing. Table S1: Information of all samples. Table S2: The filtering criteria for sites of all tissues. Table S3: Primer information for RNA editing validation. Table S4: Primer information of vector construction. Table S5: Information of all RNA editing sites. Table S6: Specificity of A-to-I editing sites in skeletal muscle of pigs. Table S7: Specificity of A-to-I editing sites of skeletal muscle with GO annotation. Table S8: The result of the prediction of miRNA target regions by miranda software.</span></p>
A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs
<p>Figure S1: PCA analysis of all tissues. Figure S2: wild(CFLAR-A) and experimental(CFLAR-G) plasmid by PCR and Sanger sequencing. Figure S3: Validation of RNA editing by PCR and Sanger sequencing. Table S1: Information of all samples. Table S2: The filtering criteria for sites of all tissues. Table S3: Primer information for RNA editing validation. Table S4: Primer information of vector construction. Table S5: Information of all RNA editing sites. Table S6: Information of all RNA-seq expression data. Table S7: Specificity of A-to-I editing sites in skeletal muscle of pigs. Table S8: Specificity of A-to-I editing sites of skeletal muscle with GO annotation. Table S9: The result of the prediction of miRNA target regions by miranda software.</p>
A synthetic RNA editing factor edits its target site in chloroplasts and bacteria
<p><span><span><span><span><span><span><span><span><span><span><span>Members of the pentatricopeptide repeat (PPR) protein family act as specificity factors in C-to-U RNA editing. The expansion of the PPR superfamily in plants provides the sequence variation required for design of consensus-based RNA-binding proteins. We used this approach to design a synthetic RNA editing factor to target one of the sites in the <i>Arabidopsis</i> chloroplast transcriptome recognised by the natural editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that our synthetic editing factor specifically recognises the target sequence in in vitro binding assays. The designed factor is equally specific for the target <i>rpoA</i> site when expressed in chloroplasts and in the bacterium <i>E. coli</i>. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins. </span></span></span></span></span></span></span></span></span></span></span></p>
Clinical Validation Study for EDIT-B Test: an Aid for Differential Diagnosis of Bipolar Disorder, Based on RNA Editing Blood Biomarkers
ClinicalTrials.gov study NCT05603819. IPD Sharing: NO. Countries: 3. Publications: 29.
A synthetic RNA editing factor edits its target site in chloroplasts and bacteria
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RECODE: a programmable guide-free C-to-U RNA editing tool
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Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes
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The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity
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Data from: The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing
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RNA sequencing quantitative analysis of RNA editing levels in ADAR1, ADAR2, AIMP2 overexpression and wild type HEK293 cells
GEO Series GSE87198. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.