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

Shuja Majeed published a dataset on figshare in 2026 containing single-cell transcriptomic profiling data from chickens. The data likely includes results from spectral flow cytometry and scRNA-seq of intraepithelial lymphocytes from 50 specific-pathogen free chicks, challenged with Salmonella Enteritidis. The study aimed to characterize innate-like cytotoxic T cell responses in the intestinal epithelium at 2 and 6 days post-infection.

Use Cases

• Identify transcriptional signatures of innate-like cytotoxic T cells based on scRNA-seq cluster analysis described.
• Analyze the expansion of TCRγδ+CD8αβ+ cytotoxic IELs based on flow cytometry results mentioned.
• Study the trajectory of T cell differentiation from progenitor to effector states using inferred trajectory analysis.
• Investigate the role of stem-like resident memory T cells as a reservoir during infection as suggested by the findings.

Strengths

• Data integrates results from two complementary techniques: spectral flow cytometry and single-cell RNA sequencing.
• Study design includes a controlled challenge with a specific dose (1.62 × 10^8 CFU/bird) and two time points (2 and 6 dpi).
• Dataset is openly available under a CC-BY-4.0 license, facilitating reuse.

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 (28.2 KB), indicating it likely contains summary or processed results rather than raw sequencing data.

Provenance

Source

figshare, author Shuja Majeed.

Collection Method

Data generated from a controlled laboratory study using spectral flow cytometry and single-cell RNA sequencing.

Time Range

Samples collected on days 2 and 6 post-infection.

Freshness

Last updated 2026-06-03 04:49:23; freshness should be verified.