LSTrAP-Kingdom

LSTrAP-Kingdom processes large-scale RNA-seq data from plants, animals, bacteria, and fungi across over two million publicly available experiments to produce annotated gene expression matrices for comparative and functional genomics.

Key Features:

• High-Throughput Processing: Demonstrated processing of 134,521 RNA-seq samples with an observed throughput of approximately 12,000 processed samples per day.
• Data Acquisition: Automated downloading of public RNA-seq experiments from repositories encompassing plants, animals, bacteria, and fungi.
• Quality Control and Annotation: Implements rigorous quality control and sample annotation to generate annotated gene expression matrices comparable to manually curated data.
• Cross-Species Analysis: Supports simultaneous analysis of RNA-seq data across multiple species and kingdoms to enable comparative studies and cross-species comparisons.
• Automation and Implementation: Pipeline automation implemented using Python and Bash scripts for end-to-end processing.

Scientific Applications:

• Systems Biology: Generation of large-scale expression matrices to support reconstruction and analysis of gene regulatory networks.
• Comparative Genomics: Comparative analyses across species and kingdoms to investigate evolutionary relationships and conserved expression patterns.
• Gene Function Inference: Identification of functionally related genes and modules through co-expression and annotated expression profiles.
• Evolutionary Studies: Large-scale cross-kingdom expression data to support evolutionary and phylogenomic investigations.

Methodology:

Implemented with Python and Bash; automated downloading of RNA-seq data, quality control, sample annotation, and generation of annotated gene expression matrices.