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A Comparison of Low Read Depth QuantSeq 3 ' Sequencing to Total RNA-Seq in FUS Mutant Mice

Jarvis, S; Birsa, N; Secrier, M; Fratta, P; Plagnol, V; (2020) A Comparison of Low Read Depth QuantSeq 3 ' Sequencing to Total RNA-Seq in FUS Mutant Mice. Frontiers in Genetics , 11 , Article 562445. 10.3389/fgene.2020.562445. Green open access

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Abstract

Transcriptomics is a developing field with new methods of analysis being produced which may hold advantages in price, accuracy, or information output. QuantSeq is a form of 3′ sequencing produced by Lexogen which aims to obtain similar gene-expression information to RNA-seq with significantly fewer reads, and therefore at a lower cost. QuantSeq is also able to provide information on differential polyadenylation. We applied both QuantSeq at low read depth and total RNA-seq to the same two sets of mouse spinal cord RNAs, each comprised by four controls and four mutants related to the neurodegenerative disease amyotrophic lateral sclerosis. We found substantial differences in which genes were found to be significantly differentially expressed by the two methods. Some of this difference likely due to the difference in number of reads between our QuantSeq and RNA-seq data. Other sources of difference can be explained by the differences in the way the two methods handle genes with different primary transcript lengths and how likely each method is to find a gene to be differentially expressed at different levels of overall gene expression. This work highlights how different methods aiming to assess expression difference can lead to different results.

Type: Article
Title: A Comparison of Low Read Depth QuantSeq 3 ' Sequencing to Total RNA-Seq in FUS Mutant Mice
Open access status: An open access version is available from UCL Discovery
DOI: 10.3389/fgene.2020.562445
Publisher version: https://doi.org/10.3389/fgene.2020.562445
Language: English
Additional information: © 2020 Jarvis, Birsa, Secrier, Fratta and Plagnol. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Keywords: RNA, ALS, bioinformatics, RNA-Seq, Fused in sarcoma, QuantSeq
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10118460
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