Study Design
Experimental Approach
Laser capture microdissection (LCM) combined with bulk RNA-seq was used to profile transcriptional changes during the critical epileptogenic window in the GAERS model.
- Comparison: Ga30 (P30, seizure-onset) vs Ga15 (P15, pre-seizure)
- Sample Size: 5 Ga30 samples, 2 Ga15 samples
- Library Prep: Takara SMARTer Stranded Total RNA-Seq Kit v3
- Sequencing: Illumina platform
- Analysis: DESeq2 differential expression
Key Findings
593 Differentially Expressed Genes
- 560 upregulated (94.4%)
- 33 downregulated (5.6%)
- Thresholds: padj < 0.1, |log2FC| > 0.5
Biological Significance: The predominant upregulation indicates active neuronal maturation and circuit development during the transition from pre-seizure to seizure-prone state.
Summary Statistics
Volcano Plot
Differential Expression Overview (Ga30 vs Ga15)
Interpretation: Each point represents a gene. Red points are significantly upregulated, blue points are significantly downregulated. Distance from center indicates magnitude of change and statistical significance.
Top Differentially Expressed Genes
Top 20 Upregulated Genes
Top 20 Downregulated Genes
Top 10 Most Significant Genes
| Rank | Gene Symbol | Gene Name | Log2FC | Adj. P-value | Regulation |
|---|
GO Enrichment Analysis
Top Enriched Biological Processes
Key Enriched Pathways
Synaptic Organization:
- Cell junction maintenance
- Postsynaptic density organization
- Regulation of synaptic plasticity
Calcium & Ion Channels:
- Calcium homeostasis
- IP3 signaling
- Voltage-gated ion channels
Biological Interpretation
Major Findings
- Predominant Upregulation (94.4%): The overwhelming majority of DEGs show increased expression at P30, indicating active transcriptional programs associated with neuronal maturation and circuit development during the epileptogenic window.
- Synaptic Plasticity & Organization: Strong enrichment in postsynaptic density organization, synaptic plasticity, and maintenance of synaptic structures reflects critical circuit refinement occurring as GAERS rats transition to seizure-prone state.
- Calcium Signaling Dysregulation: Enrichment in calcium homeostasis and ion channel genes, including T-type calcium channels (Cacna1g, Cacna1h), aligns with known mechanisms of absence seizure generation in thalamocortical circuits.
- Glutamatergic Transmission: Upregulation of NMDA receptor components and glutamatergic signaling genes consistent with thalamocortical hyperexcitability in GAERS.
Clinical Relevance
These transcriptional changes identify potential therapeutic targets for preventing or modulating absence seizure development. The prominent synaptic and ion channel dysregulation provides molecular evidence for circuit-level dysfunction underlying epileptogenesis.
Download Data
Access the complete differential expression results and processed data: