Salmo trutta Immune Cell Marker Genes and Expression Analysis

Additional file 2 from a single-cell RNA sequencing study of river brown trout (Salmo trutta fario) provides gene lists for cell type identification and differential expression analysis. The dataset includes marker genes for 23 immune cell clusters, 175 ohnologue pairs from a whole genome duplication event, and genes differentially expressed in hatchery-origin fish. It supports research on teleost immunology, evolutionary divergence, and the transcriptional impact of aquaculture environments.

Use Cases

• Identifying immune cell types in salmonids based on prior and de novo marker gene lists.
• Analyzing gene expression divergence between ohnologue pairs resulting from salmonid-specific whole genome duplication.
• Investigating hatchery-induced transcriptional changes by examining genes differentially expressed in 'farm' or 'mix' origin fish relative to 'wild'.
• Performing functional enrichment analysis using compiled Gene Ontology (GO) term outputs for high-abundance markers.

Strengths

• Contains detailed annotations for marker genes across 23 distinct immune cell clusters.
• Includes analysis of 175 ohnologue pairs, providing data on evolutionary divergence post-duplication.
• Dataset is openly licensed under CC-BY-4.0, facilitating reuse.
• Cross-platform presence on figshare indicates established use and importance.

Limitations

• Column names and exact row counts are not specified in the provided metadata, limiting precise structural understanding.
• The dataset consists of supplementary tables from a specific study, so its utility is tied to that research context.
• Metadata lacks information on the organization of the author and the specific methods of data generation beyond the analysis pipeline described.

Provenance

Source

James Ord

Collection Method

Data generated from single-cell RNA sequencing of river brown trout (Salmo trutta fario) immune cells, analyzed using Seurat.

Freshness

Last updated on 2026-03-18.