Transcriptome Profiling after Early Spinal Cord Injury in the Axolotl and Its Comparison with Rodent Animal Models through RNA-Seq Data Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Collection
2.2. Data Pre-Processing
2.3. Differential Gene Expression Analysis
2.4. Gene Ontology Analysis
2.5. Code Availability
3. Results and Discussion
3.1. Changes in the Global Gene Expression after Traumatic SCI Show Large Differences between Axolotls and Rodents
3.2. Top Regulated Genes in Axolotl and Rodents in the Acute and Sub-Acute Stages of SCI
3.3. Gene Ontology Analysis Shows Differences and Similarities in Biological Processes between Axolotl and Rodents after Traumatic SCI
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Sequencing Platform | Type of Induced Injury | Samples | Reference |
---|---|---|---|---|
Axolotl | Illumina HiSeq 2500 paired end sequencing | The spinal cord was crushed at multiple levels, including the thoracic portion | Intact spinal cord, 1 dpi and 6 dpi | [15] |
Rat | Illumina NovaSeq 6000 paired end sequencing | Lateral compression at the thoracic vertebrae T10 level | Intact spinal cord, 1 dpi and 7 dpi | [16] |
Mouse | Illumina HiSeq 2000 paired end sequencing | Contusive injury at the thoracic vertebrae T9 level | Intact spinal cord, 2 dpi and 7 dpi | [17] |
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González-Orozco, J.C.; Escobedo-Avila, I.; Velasco, I. Transcriptome Profiling after Early Spinal Cord Injury in the Axolotl and Its Comparison with Rodent Animal Models through RNA-Seq Data Analysis. Genes 2023, 14, 2189. https://doi.org/10.3390/genes14122189
González-Orozco JC, Escobedo-Avila I, Velasco I. Transcriptome Profiling after Early Spinal Cord Injury in the Axolotl and Its Comparison with Rodent Animal Models through RNA-Seq Data Analysis. Genes. 2023; 14(12):2189. https://doi.org/10.3390/genes14122189
Chicago/Turabian StyleGonzález-Orozco, Juan Carlos, Itzel Escobedo-Avila, and Iván Velasco. 2023. "Transcriptome Profiling after Early Spinal Cord Injury in the Axolotl and Its Comparison with Rodent Animal Models through RNA-Seq Data Analysis" Genes 14, no. 12: 2189. https://doi.org/10.3390/genes14122189
APA StyleGonzález-Orozco, J. C., Escobedo-Avila, I., & Velasco, I. (2023). Transcriptome Profiling after Early Spinal Cord Injury in the Axolotl and Its Comparison with Rodent Animal Models through RNA-Seq Data Analysis. Genes, 14(12), 2189. https://doi.org/10.3390/genes14122189