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Differential Expression Analysis of Stress Response Genes Using RNA-Seq

RNA-SeqTranscriptomicsStress Response

Abstract

This study presents a comprehensive RNA-Seq analysis investigating differential gene expression patterns in response to oxidative stress conditions. Using next-generation sequencing technology, we characterized transcriptional changes across multiple time points, revealing novel regulatory pathways and potential therapeutic targets for stress-related disorders.

Methods

Experimental Workflow

┌──────────┐     ┌──────────┐     ┌──────────┐     ┌────────┐
│  Sample  │────▶│   RNA    │────▶│  cDNA    │────▶│  NGS   │
│  Prep    │     │ Extract  │     │ Library  │     │  Seq   │
└──────────┘     └──────────┘     └──────────┘     └────┬───┘
                                                        │
                 ┌──────────┐     ┌──────────┐          │
                 │ DESeq2   │◀────│ Align &  │◀─────────┘
                 │ Analysis │     │ Count    │
                 └──────────┘     └──────────┘

Total RNA was extracted using the TRIzol method and quality assessed via Bioanalyzer. Libraries were prepared using the Illumina TruSeq RNA Library Prep Kit and sequenced on the NovaSeq 6000 platform generating 150bp paired-end reads. Reads were aligned to the reference genome using STAR aligner, and differential expression analysis was performed using DESeq2 with an adjusted p-value threshold of 0.05.

Key Findings

  • •Identified 1,247 differentially expressed genes under oxidative stress conditions
  • •Discovered novel transcription factor binding sites in stress response promoters
  • •Characterized temporal dynamics of antioxidant gene expression
  • •Validated findings using qRT-PCR for 15 candidate genes

Conclusion

Our comprehensive transcriptomic analysis provides new insights into the molecular mechanisms underlying cellular stress responses. The identified gene signatures and regulatory networks offer promising targets for developing therapeutic interventions for oxidative stress-related pathologies.