INSPEcT

INSPEcT estimates synthesis, processing, and degradation rates of pre-mRNA and mRNA from 4sU-seq and RNA-seq time-course data to analyze RNA dynamics and transcriptional regulation.

Key Features:

• Gene-Level Quantification: Performs gene-level quantification of pre-mRNA synthesis, pre-mRNA processing, and mRNA degradation rates.
• Data Integration: Integrates 4sU-seq and RNA-seq time-course data for joint analysis of RNA dynamics.
• Modeling Framework: Incorporates a modeling framework to identify whether synthesis, processing, or degradation account for observed changes in mRNA and pre-mRNA concentrations.
• Implementation: Provided as an R package.
• Synthetic Dataset Testing: Performance has been tested on synthetic datasets to guide modeling parameter selection and experimental design.

Scientific Applications:

• Transcriptional Regulation: Dissect contributions of synthesis, processing, and degradation to gene expression changes.
• mRNA Turnover and Stability: Analyze dynamics of mRNA turnover and stability.
• Condition Comparison: Assess the impact of biological conditions or treatments on RNA synthesis, processing, and degradation.

Methodology:

Integrates 4sU-seq and RNA-seq time-course data, performs gene-level quantification of pre-mRNA and mRNA, applies a modeling framework to infer synthesis, processing, and degradation rates, and validates performance using synthetic datasets; implemented as an R package.