Codon-Mediated Gene Expression Data for Four Model Species

Daisuke Tsugama's repository contains processed datasets and code for analyzing codon-mediated gene expression regulation. The 2.2 GB collection includes RNA-seq and Ribo-seq data, predicted expression indices, and observed TPM, mRNA half-life, and protein abundance for Arabidopsis thaliana, Oryza sativa, Homo sapiens, and Mus musculus. It was last updated on May 27, 2026.

Use Cases

• Train regression models for gene expression prediction based on codon weight metrics.
• Compare codon demand and supply dynamics across plant and animal species.
• Analyze ribosome stalling profiles from Ribo-seq data.
• Correlate mRNA half-life and protein abundance with codon usage indices.
• Visualize interspecies codon weight patterns using heatmaps and UMAP.

Strengths

• Includes data from four model species: A. thaliana, O. sativa, H. sapiens, and M. musculus.
• Provides complete computational pipelines for RNA-seq and Ribo-seq processing.
• Contains a master metadata file with NCBI accession numbers, species, tissues, and experimental conditions.
• Dataset size is 2.2 GB, indicating substantial processed data.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect bias inherent to the specific experimental conditions aggregated from public repositories.

Provenance

Source

figshare

Collection Method

Processed from public RNA-seq and Ribo-seq datasets, as indicated by the master accession list referencing NCBI GEO/SRA.

Freshness

Last updated 2026-05-27 10:36:33; freshness should be verified.