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Effect of overexpression of A3B and RNA editing calling in mouse tissues [RNA-seq]

ABSTRACT: Effect of overexpression of A3B and RNA editing calling in mouse tissues [RNA-seq]

PROVIDER: PRJNA862154 | ENA |

REPOSITORIES: ENA

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Effect of overexpression of A3B and RNA editing calling in mouse tissues [WES]

Project description:To test if A3B has RNA editing activity we performed SNV calling from WES of 8 mouse livers (Samples 1-8) and 8 pancreas (Samples 7-16)

2023-07-25 | GSE209722 | GEO

Effect of overexpression of A3B and RNA editing calling in mouse tissues [RNA-seq]

Project description:To test if A3B has RNA editng activity we performed SNV calling from RNA-seq of 6 mouse lungs (Samples 7-12), 8 mouse livers (Samples 14-20) and 8 pancreas (Samples 21-28) We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 mouse livers (Samples 1-6), 6 mouse lungs (Samples 7-12), 8 mouse livers (Samples 14-20) and 8 pancreas (Samples 21-28)

2023-07-25 | GSE209721 | GEO

Effect of overexpression of A3B and RNA editing calling in mouse tissues

Project description:Effect of overexpression of A3B and RNA editing calling in mouse tissues

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Effect of overexpression of A3B and RNA editing calling in mouse tissues [WES]

Project description:Effect of overexpression of A3B and RNA editing calling in mouse tissues [WES]

| PRJNA862153 | ENA

Effect of overexpression of A3B and RNA editing calling in mouse tissues

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-07-25 | GSE209723 | GEO

Effect of depletion of A3B on gene expression of 92.1 cells and overexpression of A3B on gene expression of MEL290 cells

Project description:To investigate the function of A3B, we established 92.1 cell lines with A3B knocked down and MEL290 cell lines with A3B overexpression. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cell lines with two replicates.

2023-06-07 | GSE218751 | GEO

Detection of APOBEC3B-mediated RNA editing sites in T-47D cells [RNA-seq]

Project description:RNA editing is a crucial post-transcriptional process that diversifies proteomic outcomes and influences gene expression. Particularly, the APOBEC3 family has emerged as a significant player in this mechanism, with APOBEC3A (A3A) showing notable roles in immune response and stress conditions. APOBEC3B (A3B), another family member, has garnered attention for its potential role in breast cancer genomic mutations. In this study, we employ an inducible expression cell model and a novel methodology for identifying differential variants in RNA (DVRs) to map A3B-mediated RNA editing sites in a breast cancer cell model. Our findings indicate that A3B engages in selective RNA editing and targets NEAT1 and MALAT1 long non-coding RNAs. Notably, the binding of these RNAs sequesters A3B’s catalytic activity, and thereby affects A3A’s activity through a feedback loop.

2024-08-14 | GSE245700 | GEO

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Project description:FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

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Decoding the Genes that A3B regulated

Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for A3B in OMM2.3 and 92.1 cells.

2023-06-07 | GSE218753 | GEO

The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome

Project description:Purpose: The purpose of this experiment is to expand the repertoire of C. elegans edited transcripts and identify the roles of ADR-1 as indirect regulator of editing and ADR-2 as the only active deaminase in vivo. Methods: Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by a novel RNA variant calling and comparative analysis pipeline. Results: Despite lacking deaminase function, ADR-1 affects editing of over 60 adenosines within the 3’ UTRs of 16 different mRNAs. Furthermore, ADR-1 interacts directly with ADR-2 substrates, even in the absence of ADR-2; and mutations within its dsRNA binding domains abolished both binding and editing regulation. Conclusions: ADR-1 acts as a major regulator of editing by binding ADR-2 substrates in vivo and raises the possibility that other dsRNA binding proteins, including the inactive human ADARs, regulate RNA editing by deaminase-independent mechanisms. Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by a novel RNA variant calling and comparative analysis pipeline.

2014-01-20 | E-GEOD-51556 | biostudies-arrayexpress

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