Pepper Cell Atlas: Single-Nucleus and Spatial Transcriptomics of Chili Fruit Development

332,468 high-quality cells from 57 samples spanning seedlings to mature fruits of chili pepper (Capsicum annuum L.) were profiled using single-nucleus RNA sequencing and spatial transcriptomics. The atlas, created by wenjun ji and last updated in April 2026, maps metabolic genes to specific cell types and spatial regions. It identifies laminar patterning transcription factors linked to localized capsanthin accumulation.

Use Cases

• Study laminar control of specialized metabolism based on the spatiotemporal single-nucleus atlas.
• Identify cell-type-specific gene expression patterns based on the mapping of metabolic genes to defined cell types.
• Investigate the role of transcription factors like WRKY6, ZAT10, and BTF3 based on their correlation with capsanthin accumulation.
• Perform comparative genomics studies across species based on the provided reference atlas.

Strengths

• Profiles 332,468 high-quality cells, providing a substantial single-cell resolution dataset.
• Integrates two complementary techniques: single-nucleus RNA sequencing and spatial transcriptomics.
• Covers 57 samples across multiple developmental stages from seedlings to mature fruits.
• Openly accessible via a dedicated web portal (http://Pepper-Cell-Atlas.com).

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect temporal or methodological bias inherent to the specific experimental setup.

Provenance

Source

figshare

Collection Method

Single-nucleus RNA sequencing and spatial transcriptomics of Capsicum annuum samples.

Time Range

Samples span from seedlings to mature fruits; specific collection dates are not provided.

Freshness

Last updated 2026-04-22 02:29:02; freshness should be verified.