PSDX

PSDX aggregates multi-omics datasets from Populus trichocarpa stem differentiating xylem under diverse stresses to enable analysis of gene expression, co-expression networks, differential expression, and post-transcriptional regulation (alternative splicing, alternative polyadenylation, alternative transcription initiation).

Key Features:

• Multi-Omics Integration: Consolidates 144 RNA-Seq libraries, 33 ChIP-seq libraries, and six single-molecule real-time (SMRT) Iso-Seq libraries derived from Populus trichocarpa tissues under different stresses.
• Unified Analysis Parameters: Applies consistent parameters for gene expression quantification, co-expression network construction, and differential expression (DEG) analysis across datasets.
• Post-Transcriptional Regulation Data: Provides pre-processed information on alternative splicing (AS), alternative polyadenylation (APA), and alternative transcription initiation (ATI).
• Gene Family Emphasis: Highlights RNA-binding protein families and stress-related genes relevant to secondary growth and stress responses.

Scientific Applications:

• Secondary Growth and Stress Response: Investigating molecular responses of stem differentiating xylem to diverse stresses in Populus trichocarpa.
• Wood Formation Mechanisms: Dissecting gene expression and regulatory networks underlying wood formation and secondary xylem differentiation.
• Post-Transcriptional Regulation Studies: Assessing the impact of AS, APA, and ATI on gene function under stress conditions.
• Comparative Expression Analyses: Comparing gene expression profiles and co-expression networks across treatments and studies using standardized analysis parameters.
• Applied Forestry and Agriculture: Informing strategies to improve stress tolerance in woody plants with potential applications in forestry and agriculture.

Methodology:

Integration of 144 RNA-Seq, 33 ChIP-seq, and six SMRT Iso-Seq libraries; unified computational analysis for gene expression quantification, co-expression network construction, and DEG detection; preprocessing to extract AS, APA, and ATI events.