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mRNA Decay pp 111–129Cite as

Integration of ENCODE RNAseq and eCLIP Data Sets

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1720))

Abstract

During the last decade, the study of mRNA decay has largely benefited from an increasing number of high-throughput assays that emerged from developments in next generation sequencing (NGS) technologies as well as mass spectrometry. While assay-specific data analysis is often reported and software made available many researchers struggle with the overwhelming challenge of integrating data from diverse assays, different sources, and of different formats.

We here use Python, R, and bash to analyze and integrate RNAseq and eCLIP data publicly available from ENCODE. Annotation is performed with biomart, motif analysis with MEME and finally a functional enrichment analysis using DAVID. This analysis is centered on KHSRP eCLIP data from K562 cell as well as RNAseq data from KHSRP knockdown and respective mock controls.

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Acknowledgments

ENCODE Consortium, the labs of Brenton Graveley at UConn and Gene Yeo at UCSD for generating the KHSRP knockdown and eCLIP data respectively.

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Authors and Affiliations

  1. Bioinformatics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany

    Jorge Boucas

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  1. Jorge Boucas
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Correspondence to Jorge Boucas .

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Editors and Affiliations

  1. Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia

    Shireen R. Lamandé

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Boucas, J. (2018). Integration of ENCODE RNAseq and eCLIP Data Sets. In: Lamandé, S. (eds) mRNA Decay. Methods in Molecular Biology, vol 1720. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7540-2_8

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  • DOI: https://doi.org/10.1007/978-1-4939-7540-2_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7539-6

  • Online ISBN: 978-1-4939-7540-2

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