What is the ABC Atlas?

The ABC Atlas is an online, browser-based tool that allows researchers to visualize multiple high-quality single-cell datasets for free – including single-cell transcriptomics (scRNAseq) & spatial transcriptomics for mice, humans, Alzheimer’s Disease, and more.

To help students understand this rich but complex data, this guide includes the following:

• Background information explaining the ABC Atlas’s terminology (e.g., scRNAseq, cell type, transcriptomics)
• A beginner-friendly user interface manual
• An example walkthrough that shows how scientists can use the ABC Atlas to ask a specific research question
• A guide on how to formulate a research question, which includes a flowchart helping you select the best ABC Atlas dataset to address your question

Want to learn more?

Check out these published articles for a more in-depth look at the datasets included within the ABC Atlas:  

• A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain (Yao et al., 2023)  

• Transcriptomic diversity of cell types across the adult human brain (Siletti et al., 2023)  

• Integrated multimodal cell atlas of Alzhiemer’s disease (Gabitto et al., 2024)