Single-Cell RNA Sequencing of Chicken Intestinal Immune Cells During Salmonella Infection

Single-cell transcriptomic data from a study of Salmonella Enteritidis infection in chickens. The dataset was generated by Shuja Majeed and published on figshare under a CC-BY-4.0 license, with a last update in June 2026. It likely contains gene expression profiles from intraepithelial lymphocytes collected from 50 specific-pathogen free chicks at 2 and 6 days post-infection.

Use Cases

• Analyzing innate-like cytotoxic T cell expansion based on scRNA-seq cluster identification mentioned in the description
• Studying transcriptional trajectories from progenitor T cells to effector cells based on the inferred trajectory analysis
• Correlating flow cytometry findings with gene expression signatures based on the integrated data approach described

Strengths

• Data integrates spectral flow cytometry and single-cell RNA sequencing from a controlled challenge study
• Study design includes 50 specific-pathogen free chicks with 25 per control and infected group
• Analysis identified specific T cell clusters, including progenitor and innate-like cytotoxic T cells, expanding post-infection

Limitations

• Row count is unknown, which may limit suitability assessment
• Column-level documentation is absent; field semantics must be inferred after download
• The dataset is small at 28.2 KB, indicating limited scope

Provenance

Source

figshare

Collection Method

Single-cell RNA sequencing and spectral flow cytometry performed on intraepithelial lymphocytes from Salmonella-challenged and control chickens.

Time Range

Samples collected at 2 and 6 days post-infection.

Freshness

Last updated 2026-06-03 04:51:10; freshness should be verified