New Guide for Creating Single-Cell Atlases

A research team led by Dr. Malte Lücken, DZL scientist at Helmholtz Munich (DZL site CPC-M), has published a guide for creating single-cell atlases in the renowned journal Nature Methods. These atlases are essential tools for mapping the diversity of cells within tissues and enable new insights into biomedical research and therapeutic development.

Thanks to single-cell RNA sequencing, scientists can analyze tissues at the cellular level in great detail. In recent years, numerous datasets have been created, often focusing narrowly on specific questions. To obtain a more comprehensive picture of cellular diversity in organs and between individuals, these data are integrated into "atlases."

These atlases serve as reference works for tissue biology, providing standardized labels for cell types and important insights for research. However, the approaches to creating such atlases vary significantly, leading to differences in quality. This is where the new publication comes in.

The published guide offers detailed recommendations on how to create single-cell atlases that meet the highest scientific standards. "Atlases are more than just data collections—they are fundamental tools that drive research forward," explains Karin Hrovatin, first author of the study. Her co-author Lisa Sikkema adds, "With our guide, we aim to support researchers worldwide in creating high-quality atlases and opening up new possibilities in tissue biology."

The study also emphasizes the importance of single-cell atlases for international collaboration. "Our goal is to create a common framework that not only advances individual studies but unites the global research community," says Dr. Malte Lücken, senior author of the study.

Source: Helmholtz Munich Researchers Publish Guide to Single-Cell Atlases

Original publication:
Hrovatin K, Sikkema L, Shitov VA, Heimberg G, Shulman M, Oliver AJ, Mueller MF, Ibarra IL, Wang H, Ramírez-Suástegui C, He P, Schaar AC, Teichmann SA, Theis FJ, Luecken MD. Considerations for building and using integrated single-cell atlases. Nat Methods. 2025 Jan;22(1):41-57. doi: 10.1038/s41592-024-02532-y. Epub 2024 Dec 13. PMID: 39672979.