Quantification of gene expression while taking into account RNA alternative splicing.
Gene expression quantification
Microarray
Quantitative real-time PCR
RNA alternative splicing
RNA sequencing
Journal
Genomics
ISSN: 1089-8646
Titre abrégé: Genomics
Pays: United States
ID NLM: 8800135
Informations de publication
Date de publication:
12 2019
12 2019
Historique:
received:
12
09
2018
accepted:
16
10
2018
pubmed:
27
10
2018
medline:
2
5
2020
entrez:
27
10
2018
Statut:
ppublish
Résumé
Gene expression has been widely used in functional genomics research; however, the gene expressions quantified with different methods have been frequently inconsistent, thus challenging the conclusions from such research. Here we have addressed this issue, while taking into account RNA alternative splicing. We found that when a gene was subjected to RNA alternative splicing, it was impossible or difficult to properly quantify the expression of a transcript of the gene or its overall expression using quantitative real-time PCR (qPCR), Northern hybridization, microarray, or serial analysis of gene expression. Shot-gun RNA-seq was the most proper to quantify the expression of a transcript or a gene in such cases. Moreover, the expressions of individual transcripts quantified by shot-gun RNA-seq were highly reproducible (r = 0.90-0.98) between individuals. Therefore, shot-gun or full-length RNA-seq should be the method of choice to properly quantify the expression of a transcript or a gene.
Identifiants
pubmed: 30366041
pii: S0888-7543(18)30533-0
doi: 10.1016/j.ygeno.2018.10.009
pii:
doi:
Substances chimiques
Plant Proteins
0
RNA, Plant
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1517-1528Informations de copyright
Copyright © 2018 Elsevier Inc. All rights reserved.