Single-Cell Transcriptomic Profiling of Chicken Immune Cells During Salmonella Infection

50 specific-pathogen free chicks were used in a study examining immune responses to Salmonella Enteritidis infection at 2 and 6 days post-infection. The dataset, published by Shuja Majeed on figshare under CC-BY-4.0, integrates spectral flow cytometry and single-cell RNA sequencing results. It reveals the expansion of innate-like cytotoxic intraepithelial lymphocytes as a key early defense mechanism.

Use Cases

• Analyzing transcriptional signatures of innate-like cytotoxic T cells based on scRNA-seq cluster identification.
• Studying the trajectory of T cell differentiation from progenitor to effector states based on inferred trajectory analysis.
• Investigating the role of TCRγδ+CD8αβ+ cytotoxic intraepithelial lymphocytes in response to bacterial challenge based on flow cytometry results.
• Examining the functional reprogramming of cytotoxic T cells within the intestinal epithelial compartment based on integrated flow cytometry and scRNA-seq data.

Strengths

• Integrates two complementary data types: spectral flow cytometry and single-cell RNA sequencing.
• Includes data from a controlled challenge with Salmonella Enteritidis at a dose of 1.62 × 10^8 CFU/bird.
• Provides results from two distinct time points: 2 and 6 days post-infection.
• Based on a study cohort of 50 specific-pathogen free chicks, with 25 per experimental group.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The dataset is small in size (53.7 KB), suggesting limited scope or summary-level data.

Provenance

Source

figshare

Collection Method

Data generated via spectral flow cytometry and single-cell RNA sequencing of intraepithelial lymphocytes from chicken ileum.

Time Range

Samples collected on day 2 and day 6 post-infection.

Freshness

Last updated 2026-06-03 04:49:19; freshness should be verified.