NormQ: RNASeq normalization based on RT-qPCR derived size factors

NormQ: RNASeq normalization based on RT-qPCR derived size factors

The merit of RNASeq data relies heavily on correct normalization. However, most methods assume that the majority of transcripts show no differential expression between conditions. This assumption may not always be correct, especially when one condition results in overexpression. We present a new met...

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Main Authors: Ravindra Naraine, Pavel Abaffy, Monika Sidova, Silvie Tomankova, Kseniia Pocherniaieva, Ondrej Smolik, Mikael Kubista, Martin Psenicka, Radek Sindelka
Format: Article
Language:English
Published: Elsevier 2020-01-01
Series:Computational and Structural Biotechnology Journal
Subjects:
Transcriptomics
RNASeq
Normalization
TOMOSeq
DESeq
Median-of-ratios
Online Access:http://www.sciencedirect.com/science/article/pii/S2001037020302737
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spelling doaj-c82fb33bbbb742fda12a564e7edc6dcb2021-01-02T05:08:36ZengElsevierComputational and Structural Biotechnology Journal2001-03702020-01-011811731181NormQ: RNASeq normalization based on RT-qPCR derived size factorsRavindra Naraine0Pavel Abaffy1Monika Sidova2Silvie Tomankova3Kseniia Pocherniaieva4Ondrej Smolik5Mikael Kubista6Martin Psenicka7Radek Sindelka8Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech RepublicLaboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech RepublicLaboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech RepublicLaboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech RepublicUniversity of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Vodnany, Czech RepublicLaboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech Republic; Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech RepublicLaboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech RepublicUniversity of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Vodnany, Czech RepublicLaboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec 252 50, Czech Republic; Corresponding author.The merit of RNASeq data relies heavily on correct normalization. However, most methods assume that the majority of transcripts show no differential expression between conditions. This assumption may not always be correct, especially when one condition results in overexpression. We present a new method (NormQ) to normalize the RNASeq library size, using the relative proportion observed from RT-qPCR of selected marker genes. The method was compared against the popular median-of-ratios method, using simulated and real-datasets. NormQ produced more matches to differentially expressed genes in the simulated dataset and more distribution profile matches for both simulated and real datasets.http://www.sciencedirect.com/science/article/pii/S2001037020302737TranscriptomicsRNASeqNormalizationTOMOSeqDESeqMedian-of-ratios
collection DOAJ
language English
format Article
sources DOAJ
author Ravindra Naraine
Pavel Abaffy
Monika Sidova
Silvie Tomankova
Kseniia Pocherniaieva
Ondrej Smolik
Mikael Kubista
Martin Psenicka
Radek Sindelka
spellingShingle Ravindra Naraine
Pavel Abaffy
Monika Sidova
Silvie Tomankova
Kseniia Pocherniaieva
Ondrej Smolik
Mikael Kubista
Martin Psenicka
Radek Sindelka
NormQ: RNASeq normalization based on RT-qPCR derived size factors
Computational and Structural Biotechnology Journal
Transcriptomics
RNASeq
Normalization
TOMOSeq
DESeq
Median-of-ratios
author_facet Ravindra Naraine
Pavel Abaffy
Monika Sidova
Silvie Tomankova
Kseniia Pocherniaieva
Ondrej Smolik
Mikael Kubista
Martin Psenicka
Radek Sindelka
author_sort Ravindra Naraine
title NormQ: RNASeq normalization based on RT-qPCR derived size factors
title_short NormQ: RNASeq normalization based on RT-qPCR derived size factors
title_full NormQ: RNASeq normalization based on RT-qPCR derived size factors
title_fullStr NormQ: RNASeq normalization based on RT-qPCR derived size factors
title_full_unstemmed NormQ: RNASeq normalization based on RT-qPCR derived size factors
title_sort normq: rnaseq normalization based on rt-qpcr derived size factors
publisher Elsevier
series Computational and Structural Biotechnology Journal
issn 2001-0370
publishDate 2020-01-01
description The merit of RNASeq data relies heavily on correct normalization. However, most methods assume that the majority of transcripts show no differential expression between conditions. This assumption may not always be correct, especially when one condition results in overexpression. We present a new method (NormQ) to normalize the RNASeq library size, using the relative proportion observed from RT-qPCR of selected marker genes. The method was compared against the popular median-of-ratios method, using simulated and real-datasets. NormQ produced more matches to differentially expressed genes in the simulated dataset and more distribution profile matches for both simulated and real datasets.
topic Transcriptomics
RNASeq
Normalization
TOMOSeq
DESeq
Median-of-ratios
url http://www.sciencedirect.com/science/article/pii/S2001037020302737
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