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Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture

Mahboubi, Amir and Delhomme, Nicolas and Haggstrom, Sara and Hanson, Johannes (2021). Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture. Plant Methods. 17 , 92
[Research article]

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Abstract

Background Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming. Methods and results Here we developed a platform for Ribo-Seq library construction and data analysis to enable rapid quality assessment of Ribo-Seq libraries with the help of a small-scale sequencer. Our data show that several qualitative features of a Ribo-Seq library, such as read length distribution, P-site distribution, reading frame and triplet periodicity, can be effectively evaluated using only the data generated by a benchtop sequencer with a very limited number of reads. Conclusion Our pipeline enables rapid evaluation of Ribo-Seq libraries, opening up possibilities for optimization of Ribo-Seq library construction from difficult samples, and leading to better decision making prior to more costly deep sequencing.

Authors/Creators:Mahboubi, Amir and Delhomme, Nicolas and Haggstrom, Sara and Hanson, Johannes
Title:Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
Series Name/Journal:Plant Methods
Year of publishing :2021
Volume:17
Article number:92
Number of Pages:10
Publisher:BMC
ISSN:1746-4811
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
Keywords:Ribosomal profiling, Translation, Evaluation of sequencing library quality, Translational profiling, Ribo-Seq
URN:NBN:urn:nbn:se:slu:epsilon-p-113413
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113413
Additional ID:
Type of IDID
DOI10.1186/s13007-021-00791-w
Web of Science (WoS)000687996100001
ID Code:25270
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:07 Sep 2021 15:25
Metadata Last Modified:07 Sep 2021 15:31

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