Cargando…

Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR

Molecular analyses of normal and diseased cells give insight into changes in gene expression and help in understanding the background of pathophysiological processes. Years after cDNA microarrays were established in research, RNA sequencing (RNA-seq) became a key method of quantitatively measuring t...

Descripción completa

Detalles Bibliográficos
Autores principales: Rachinger, Nicole, Fischer, Stefan, Böhme, Ines, Linck-Paulus, Lisa, Kuphal, Silke, Kappelmann-Fenzl, Melanie, Bosserhoff, Anja K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8430810/
https://www.ncbi.nlm.nih.gov/pubmed/34502254
http://dx.doi.org/10.3390/ijms22179349
_version_ 1783750791489650688
author Rachinger, Nicole
Fischer, Stefan
Böhme, Ines
Linck-Paulus, Lisa
Kuphal, Silke
Kappelmann-Fenzl, Melanie
Bosserhoff, Anja K.
author_facet Rachinger, Nicole
Fischer, Stefan
Böhme, Ines
Linck-Paulus, Lisa
Kuphal, Silke
Kappelmann-Fenzl, Melanie
Bosserhoff, Anja K.
author_sort Rachinger, Nicole
collection PubMed
description Molecular analyses of normal and diseased cells give insight into changes in gene expression and help in understanding the background of pathophysiological processes. Years after cDNA microarrays were established in research, RNA sequencing (RNA-seq) became a key method of quantitatively measuring the transcriptome. In this study, we compared the detection of genes by each of the transcriptome analysis methods: cDNA array, quantitative RT-PCR, and RNA-seq. As expected, we found differences in the gene expression profiles of the aforementioned techniques. Here, we present selected genes that exemplarily demonstrate the observed differences and calculations to reveal that a strong RNA secondary structure, as well as sample preparation, can affect RNA-seq. In summary, this study addresses an important issue with a strong impact on gene expression analysis in general. Therefore, we suggest that these findings need to be considered when dealing with data from transcriptome analyses.
format Online
Article
Text
id pubmed-8430810
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-84308102021-09-11 Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR Rachinger, Nicole Fischer, Stefan Böhme, Ines Linck-Paulus, Lisa Kuphal, Silke Kappelmann-Fenzl, Melanie Bosserhoff, Anja K. Int J Mol Sci Article Molecular analyses of normal and diseased cells give insight into changes in gene expression and help in understanding the background of pathophysiological processes. Years after cDNA microarrays were established in research, RNA sequencing (RNA-seq) became a key method of quantitatively measuring the transcriptome. In this study, we compared the detection of genes by each of the transcriptome analysis methods: cDNA array, quantitative RT-PCR, and RNA-seq. As expected, we found differences in the gene expression profiles of the aforementioned techniques. Here, we present selected genes that exemplarily demonstrate the observed differences and calculations to reveal that a strong RNA secondary structure, as well as sample preparation, can affect RNA-seq. In summary, this study addresses an important issue with a strong impact on gene expression analysis in general. Therefore, we suggest that these findings need to be considered when dealing with data from transcriptome analyses. MDPI 2021-08-28 /pmc/articles/PMC8430810/ /pubmed/34502254 http://dx.doi.org/10.3390/ijms22179349 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Rachinger, Nicole
Fischer, Stefan
Böhme, Ines
Linck-Paulus, Lisa
Kuphal, Silke
Kappelmann-Fenzl, Melanie
Bosserhoff, Anja K.
Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
title Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
title_full Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
title_fullStr Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
title_full_unstemmed Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
title_short Loss of Gene Information: Discrepancies between RNA Sequencing, cDNA Microarray, and qRT-PCR
title_sort loss of gene information: discrepancies between rna sequencing, cdna microarray, and qrt-pcr
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8430810/
https://www.ncbi.nlm.nih.gov/pubmed/34502254
http://dx.doi.org/10.3390/ijms22179349
work_keys_str_mv AT rachingernicole lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr
AT fischerstefan lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr
AT bohmeines lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr
AT linckpauluslisa lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr
AT kuphalsilke lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr
AT kappelmannfenzlmelanie lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr
AT bosserhoffanjak lossofgeneinformationdiscrepanciesbetweenrnasequencingcdnamicroarrayandqrtpcr