The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy
| Autor: | Sofie Daelemans, Jana Janssens, Debby Van Dam, Peter Paul De Deyn, René A.J. Crans, Robrecht Raedt, Kathleen Van Craenenbroeck, Elise Wouters, Christophe P. Stove |
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| Přispěvatelé: | Molecular Neuroscience and Ageing Research (MOLAR) |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Male Gene Expression Hippocampus Biochemistry Phase Determination Transcriptome Rats Sprague-Dawley 0302 clinical medicine Reference genes RAT MODEL Medicine and Health Sciences TRANSCRIPTION Short Interspersed Nucleotide Elements Mammals Brain Diseases Multidisciplinary REFERENCE Applied Mathematics Simulation and Modeling Messenger RNA Brain Eukaryota Nucleic acids Ribosomal RNA Neurology YWHAZ Vertebrates Physical Sciences Crystallographic Techniques Disease Progression Medicine Anatomy REFERENCE GENES MESSENGER-RNA Engineering sciences. Technology Algorithms Research Article EXPRESSION Cell biology Cellular structures and organelles GENES Science RNA-POLYMERASE-II Computational biology Biology Research and Analysis Methods Real-Time Polymerase Chain Reaction Rodents Temporal lobe 03 medical and health sciences Short Interspersed Nuclear Elements (SINEs) Genetics Animals B2 RNA Non-coding RNA Gene Gene Expression Profiling REAL-TIME Organisms KAINIC ACID Biology and Life Sciences Gene expression profiling Disease Models Animal 030104 developmental biology Epilepsy Temporal Lobe Amniotes RNA SEIZURES Ribosomes 030217 neurology & neurosurgery Mathematics |
| Zdroj: | PLOS ONE PLoS ONE, Vol 14, Iss 1, p e0210567 (2019) PLoS ONE PLoS ONE, 14(1):0210567. PUBLIC LIBRARY SCIENCE |
| ISSN: | 1932-6203 |
| Popis: | BackgroundIn gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression.ResultsGeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap.ConclusionIn this study, we demonstrate the potential of implementing SINEs-notably the B1 element as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression. |
| Databáze: | OpenAIRE |
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