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

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...

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Autores principales: Jarvis, Seth, Birsa, Nicol, Secrier, Maria, Fratta, Pietro, Plagnol, Vincent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7717943/
https://www.ncbi.nlm.nih.gov/pubmed/33329699
http://dx.doi.org/10.3389/fgene.2020.562445
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author Jarvis, Seth
Birsa, Nicol
Secrier, Maria
Fratta, Pietro
Plagnol, Vincent
author_facet Jarvis, Seth
Birsa, Nicol
Secrier, Maria
Fratta, Pietro
Plagnol, Vincent
author_sort Jarvis, Seth
collection PubMed
description 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.
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spelling pubmed-77179432020-12-15 A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice Jarvis, Seth Birsa, Nicol Secrier, Maria Fratta, Pietro Plagnol, Vincent Front Genet Genetics 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. Frontiers Media S.A. 2020-11-19 /pmc/articles/PMC7717943/ /pubmed/33329699 http://dx.doi.org/10.3389/fgene.2020.562445 Text en Copyright © 2020 Jarvis, Birsa, Secrier, Fratta and Plagnol. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Genetics
Jarvis, Seth
Birsa, Nicol
Secrier, Maria
Fratta, Pietro
Plagnol, Vincent
A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
title A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
title_full A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
title_fullStr A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
title_full_unstemmed A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
title_short A Comparison of Low Read Depth QuantSeq 3′ Sequencing to Total RNA-Seq in FUS Mutant Mice
title_sort comparison of low read depth quantseq 3′ sequencing to total rna-seq in fus mutant mice
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7717943/
https://www.ncbi.nlm.nih.gov/pubmed/33329699
http://dx.doi.org/10.3389/fgene.2020.562445
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