Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia–Reperfusion
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Transient Cerebral Ischemia Rat Model
2.3. Magnetic Resonance Imaging
2.4. RNA Isolation
2.5. RNA-Seq
2.6. RNA-Seq Data Analysis
2.7. Total RNA RNase R-Treatment
2.8. cDNA Synthesis
2.9. Reverse Transcription Polymerase Chain Reaction (RT–PCR)
2.10. Electrophoresis of PCR Products
2.11. Sequencing of PCR Products
2.12. Real-Time RT–PCR
2.13. Data Analysis of Real-time RT-PCR and Statistics
2.14. Functional Analysis
2.15. Construction of circ-miRNA-mRNA Network
2.16. Availability of Data and Material
3. Results
3.1. Magnetic Resonance Imaging (MRI)
3.2. RNA-Seq Analysis of circRNA Diversity in tMCAO Rat Model Conditions
3.3. RNA-Seq Analysis of Differential Expression of circRNAs at 24 h after tMCAO
3.4. Comparative Analysis of Transcriptome Profile Changes of mRNAs and circRNAs at 24 h after tMCAO
3.5. Differentially Expressed circRNAs Associated with Neurotransmitter Signaling Pathways at 24 h after tMCAO
3.6. Analysis of circRNA–miRNA–mRNA Networks Associated with the ‘Glutamatergic Synapse’ Signaling Pathway at 24 h after tMCAO
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Filippenkov, I.B.; Stavchansky, V.V.; Denisova, A.E.; Valieva, L.V.; Remizova, J.A.; Mozgovoy, I.V.; Zaytceva, E.I.; Gubsky, L.V.; Limborska, S.A.; Dergunova, L.V. Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia–Reperfusion. Genes 2021, 12, 1870. https://doi.org/10.3390/genes12121870
Filippenkov IB, Stavchansky VV, Denisova AE, Valieva LV, Remizova JA, Mozgovoy IV, Zaytceva EI, Gubsky LV, Limborska SA, Dergunova LV. Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia–Reperfusion. Genes. 2021; 12(12):1870. https://doi.org/10.3390/genes12121870
Chicago/Turabian StyleFilippenkov, Ivan B., Vasily V. Stavchansky, Alina E. Denisova, Liya V. Valieva, Julia A. Remizova, Ivan V. Mozgovoy, Elizaveta I. Zaytceva, Leonid V. Gubsky, Svetlana A. Limborska, and Lyudmila V. Dergunova. 2021. "Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia–Reperfusion" Genes 12, no. 12: 1870. https://doi.org/10.3390/genes12121870