DEPIB

DEPIB analyzes bulk RNA sequencing (RNAseq) data using a Snakemake workflow to identify differentially expressed genes across experimental conditions for studies such as pesticide-induced senescence in human mesenchymal stem cells (MSCs) and temozolomide resistance in glioblastoma (GBM).

Key Features:

• Pipeline Automation: Implements a Snakemake workflow to automate reproducible RNAseq processing steps.
• Differential Expression Analysis: Identifies genes with significant changes in expression across experimental conditions or treatments.
• Bulk RNAseq Processing: Processes bulk RNA sequencing data to compare gene expression profiles between samples.
• Integration with Metabolic and Immune Markers: Integrates transcriptomic results with protein expression analyses of metabolic markers such as MDH1, GOT, and SIRT3 and with immune function assessments.
• Secretome Functional Analysis: Supports analysis of secretome effects on cellular properties, including immunomodulation.
• Longitudinal and Integrative Analyses: Facilitates longitudinal comparisons and integration of RNAseq with other analyses to detect tolerant-like cell populations and chromatin remodeling signatures.

Scientific Applications:

• Environmental Contaminant Impact on Cellular Aging: Analyzes effects of environmental contaminants, including low-dose exposure to a mixture of seven common pesticides, on MSC transcriptomes to identify oxidative stress–induced senescence, shifts toward adipogenesis, and deterioration of immunosuppressive properties compared with aged donor samples.
• Cancer Drug Resistance Mechanisms: Characterizes gene expression changes associated with temozolomide (TMZ) resistance in glioblastoma (GBM), enabling identification of tolerant-like cell populations, chromatin remodeling events, and potential therapeutic targets.

Methodology:

DEPIB uses a Snakemake workflow to process bulk RNAseq data for differential expression analysis and integrates transcriptomic results with protein-level metabolic marker analyses and functional secretome assessments.