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Regulation of alternative splicing in Arabidopsis thaliana - a combined RNA-Seq and RIP-Seq approach

Antragstellerinnen / Antragsteller Professor Dr. Ivo Große; Professorin Dr. Dorothee Staiger
Subject Area Pflanzenphysiologie
Term from 2013 to 2018
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 237551928
 
Final Report Year 2021

Final Report Abstract

Understanding the regulation of alternative splicing in Arabidopsis thaliana requires a novel combination of experimental approaches such as RNA sequencing (RNA-seq) and RNA immunoprecipitation sequencing (RIP-seq) with computational approaches. These computational approaches include – but are not limited to – approaches for (i) the analysis of RNA-seq data, (ii) the analysis of RIP-seq data, (iii) the prediction of rhythmically expressed transcripts, (iv) the prediction of differentially used transcripts, (v) the prediction of alternatively spliced genes, and (vi) the visualization of these predictions. The goal of the bioinformatics sub-project of DFG project Regulation of alternative splicing in Arabidopsis thaliana – a combined RNA-Seq and RIP-Seq approach conducted at the Chair of Bioinformatics at the Institute of Computer Science at Martin Luther University Halle-Wittenberg was (i) to develop, to optimize, and to evaluate bioinformatics pipelines for these six tasks, (ii) to apply these six bioinformatics pipelines to the wet-lab data generated by our project partners to perform the above-mentioned predictions, and (iii) to analyse and to interpret the results of these computational predictions. All of this work (i) - (iii) was performed jointly in close collaboration with our project partners at the Chair of RNA Biology and Molecular Physiology at University Bielefeld lead by Prof. Dr. Dorothee Staiger and our lab members at the Chair of Bioinformatics at the Institute of Computer Science at Martin Luther University Halle- Wittenberg.

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