The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs
Abstract
:1. Introduction
2. Results
2.1. Identification of Differentially Expressed Genes and miRNAs
2.2. Co-Expression Modules and Enrichment Analysis
2.3. Target Genes of DE miRNAs
2.4. Temporal Dynamics of Expression
3. Discussion
4. Materials and Methods
4.1. Sample Preparation and Transcriptome Sequencing
4.2. Construction of RNA-Seq Assembly and Counts Matrix of Expression
4.3. Identification of Known and Novel miRNAs
4.4. Differential Expression of mRNAs and miRNAs
4.5. mRNA Co-Expression Network Analysis (WGCNA)
4.6. Gene Ontology Enrichment Analysis
4.7. Prediction of miRNA Target Genes and Identification of Potential miRNA–Gene Pairs
4.8. Gene Expression Trend Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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GO ID | Module Color | Annotation | p-Value | Associated Genes |
---|---|---|---|---|
GO:0045123 | Yellow | Cellular extravasation | 2.13E-05 | BST1 CCL25 CRK |
GO:0070665 | Turquoise | Positive regulation of leukocyte proliferation | 3.89E-05 | BCL6 CSF1R JAK2 PTH SYK |
GO:0002460 | Turquoise | Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 7.51E-05 | BCH2 BCL6 C1QBP JAK2 SHLD2 UNG |
GO:0051451 | Blue | Myoblast migration | 7.65E-05 | NET1 SIX4 |
GO:0002520 | Turquoise | Immune system development | 8.76E-05 | BCL6 ICOS SBDS SHLD2 UNG |
GO:0030214 | Blue | Hyaluronan catabolic process | 0.000117449 | CD44 CEMIP |
GO:0035627 | Blue | Ceramide transport | 0.000133028 | ABCA2 CPTP |
GO:0099068 | Yellow | Postsynapse assembly | 0.000403104 | CRK NLGN3 |
GO:0010810 | Yellow | Regulation of cell–substrate adhesion | 0.000552828 | BST1 CCL25 CRK |
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Zhang, Q.; Lu, B. The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs. Int. J. Mol. Sci. 2024, 25, 9225. https://doi.org/10.3390/ijms25179225
Zhang Q, Lu B. The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs. International Journal of Molecular Sciences. 2024; 25(17):9225. https://doi.org/10.3390/ijms25179225
Chicago/Turabian StyleZhang, Qi, and Bin Lu. 2024. "The mRNA and microRNA Landscape of the Blastema Niche in Regenerating Newt Limbs" International Journal of Molecular Sciences 25, no. 17: 9225. https://doi.org/10.3390/ijms25179225