Loss of gene information: Discrepancies between rna sequencing, cdna microarray, and qrt-pcr

Rachinger N, Fischer S, Böhme I, Linck-Paulus L, Kuphal S, Kappelmann-Fenzl M, Boßerhoff AK (2021)

Publication Type: Journal article

Publication year: 2021

Journal

International Journal of Molecular Sciences MDPI

Book Volume: 22

Article Number: 9349

Journal Issue: 17

DOI: 10.3390/ijms22179349

Abstract

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 quan-titatively 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.

Authors with CRIS profile

Nicole Rachinger Lehrstuhl für Biochemie und Molekulare Medizin Ines Böhme-Schäfer Lehrstuhl für Biochemie und Molekulare Medizin Lisa Linck-Paulus Lehrstuhl für Biochemie und Molekulare Medizin Silke Kuphal Medizinische Fakultät Anja Katrin Boßerhoff Lehrstuhl für Biochemie und Molekulare Medizin

Involved external institutions

Technische Hochschule Deggendorf DE Germany (DE)

How to cite

APA:

Rachinger, N., Fischer, S., Böhme, I., Linck-Paulus, L., Kuphal, S., Kappelmann-Fenzl, M., & Boßerhoff, A.K. (2021). Loss of gene information: Discrepancies between rna sequencing, cdna microarray, and qrt-pcr. International Journal of Molecular Sciences, 22(17). https://dx.doi.org/10.3390/ijms22179349

MLA:

Rachinger, Nicole, et al. "Loss of gene information: Discrepancies between rna sequencing, cdna microarray, and qrt-pcr." International Journal of Molecular Sciences 22.17 (2021).

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