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  Identification of regulatory links between transcription and RNA processing with long-read sequencing

Alfonso-Gonzalez, C., Arrigoni, L., Ozbulut, H. C., Falk, S., Bönisch, U., & Hilgers, V. (2023). Identification of regulatory links between transcription and RNA processing with long-read sequencing. STAR Protocols, 4: 102505. doi:10.1016/j.xpro.2023.102505.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000D-BAEB-9 Version Permalink: https://hdl.handle.net/21.11116/0000-000D-BAEC-8
Genre: Journal Article

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10.1016_j.xpro.2023.102505.pdf (Publisher version), 6MB
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10.1016_j.xpro.2023.102505.pdf
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Copyright Date:
2023
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The Author(s). Published by Elsevier Inc. All rights reserved.
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https://creativecommons.org/licenses/by/4.0/

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https://www.sciencedirect.com/science/article/pii/S2666166723004720?via%3Dihub (Publisher version)
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 Creators:
Alfonso-Gonzalez, Carlos1, Author
Arrigoni, Laura2, Author
Ozbulut, Hasan Can1, Author
Falk, Stefanie2, Author
Bönisch, Ulrike2, Author           
Hilgers, Valérie1, Author           
Affiliations:
1Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243642              
2Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243648              

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Free keywords: Bioinformatics; Genomics; Molecular Biology; RNAseq; Sequence Analysis; Sequencing.
 Abstract: We present a detailed protocol for sequencing full-length mRNA isoforms using the Oxford nanopore long-read sequencing technology. We describe steps for poly(A) RNA isolation, library preparation, and cDNA size selection. We then detail procedures for sequencing and processing and a computational framework to identify exon couplings and assign mRNA 5' ends and 3' ends to each other. Our approach enables the identification of links between transcription initiation and co-transcriptional RNA processing events. For complete details on the use and execution of this protocol, please refer to Alfonso-Gonzalez et al.1.

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Language(s): eng - English
 Dates: 2023-09-19
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1016/j.xpro.2023.102505
 Degree: -

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Title: STAR Protocols
Source Genre: Journal
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Publ. Info: Cambridge, MA ; Amsterdam : Cell Press ; Elsevier
Pages: - Volume / Issue: 4 Sequence Number: 102505 Start / End Page: - Identifier: ISSN: 2666-1667
CoNE: https://pure.mpg.de/cone/journals/resource/2666-1667