Table 5_Single-cell transcriptomic profiling reveals innate-like cytotoxic intraepithelial

Fifty specific-pathogen free chicks were used to generate single-cell RNA sequencing and flow cytometry data on intraepithelial lymphocyte (IEL) responses to Salmonella Enteritidis challenge. The dataset captures transcriptional profiles and cell proportions from ileal IELs at 2 and 6 days post-infection, revealing expansion of innate-like cytotoxic T cell clusters. It integrates spectral flow cytometry and scRNA-seq to examine functional reprogramming of cytotoxic T cells within the intestinal epithelium.

Use Cases

• Analyzing transcriptional signatures of innate-like cytotoxic T cells mobilized during enteric infection.
• Comparing intraepithelial lymphocyte subtype proportions between infected and control groups at specific time points.
• Investigating the functional reprogramming of TCRγδ+CD8αβ+ cytotoxic IELs via integrated multi-omics data.
• Studying early immune responses in chickens to a major foodborne pathogen (Salmonella Enteritidis).

Strengths

• Integrates two complementary high-resolution techniques: spectral flow cytometry and single-cell RNA sequencing.
• Based on a controlled in vivo challenge study with 50 animals and defined infection parameters (1.62 × 10^8 CFU/bird).
• Data is openly shared under a permissive CC-BY-4.0 license, facilitating reuse.

Limitations

• Column names and a precise row count are not provided in the available metadata, limiting immediate assessment of data structure.
• The dataset appears to be split across multiple file entries on figshare with slightly different sizes, creating potential confusion for download.
• The temporal coverage is limited to two early time points (2 and 6 days post-infection).

Provenance

Source

Research study by Shuja Majeed.

Collection Method

Experimental data from a controlled challenge of specific-pathogen free chicks with Salmonella Enteritidis, followed by IEL isolation, spectral flow cytometry, and scRNA-seq.

Time Range

Samples collected at 2 and 6 days post-infection.

Freshness

Last updated on 2026-06-03.