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Comrades-OO: An Object-Oriented R Package for Comprehensive Analysis of RNA Structure Generated using RNA crosslinking experiments

ABSTRACT: comrades-OO: An Object-Oriented R Package for Comprehensive Analysis of RNA Structure Generated using RNA crosslinking experiments

PROVIDER: PRJNA1032896 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26552124_1.fastq.gz	Fastqsanger.gz
	SRR26552124_2.fastq.gz	Fastqsanger.gz
	SRR26552125_1.fastq.gz	Fastqsanger.gz
	SRR26552125_2.fastq.gz	Fastqsanger.gz
	SRR26552126_1.fastq.gz	Fastqsanger.gz

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comrades-OO: An Object-Oriented R Package for Comprehensive Analysis of RNA Structure Generated using RNA crosslinking experiments

Project description:RNA molecules have secondary and tertiary structures in vivo which play a crucial role in various cellular processes such as the regulation of gene expression, RNA processing, and localization. Investigating these structures will enhance our understanding of their functions and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analysing complex in vivo RNA structural data. Here, we present COMRADES Object-Oriented (comrades-OO), a novel software package for the comprehensive analysis of data derived from the COMRADES experiment. comrades-OO offers a comprehensive pipeline from raw sequencing reads to the identification of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. COMRADES-OO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction.

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Project description:Determining how stem cell differentiation is controlled has important implications for understanding the etiology of degenerative disease and designing regenerative therapies. In vivo analyses of stem cell model systems have revealed regulatory paradigms for stem cell self-renewal and differentiation. The germarium of the female Drosophila gonad, which houses both germline and somatic stem cells, is one such model system. Bulk mRNA sequencing (RNA-seq), single cell (sc) RNA-seq, and bulk translation efficiency of mRNAs is available for stem cells and their differentiating progeny within the Drosophila germarium. However, visualizing those data is hampered by lack of a tool to spatially map gene expression and translational data in the germarium. Here, we have developed Oo-site (https://www.ranganlab.com/Oo-site), a tool for visualizing bulk- and scRNA-seq and translational efficiency data during different stages of germline differentiation, that makes these data accessible to non-bioinformaticians. Using this tool, we recapitulated previously reported expression patterns of developmentally regulated genes and discovered that meiotic genes, such as those that regulate the synaptonemal complex, are regulated at the level of translation.

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