Database Guide: Allen Brain Cell (ABC) Atlas
An in-depth guide for undergraduate students on how to use the Allen Brain Cell (ABC) Atlas to ask and explore research questions
About
Topics: Transcriptomics, Neuroscience, Open Dataset Guide, Independent Research Study
Audience: Advanced undergraduate students, introductory graduate students
Database: ABC Atlas
Resource type: Database/dataset guide
Materials
Background Knowledge
ABC Atlas Manual
Walkthrough Use Case Example
Formulating Research Question
Primary literature for the datasets:
Mouse, Human, Alzheimer’s Disease
Description:
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
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
Last updated May 6 2025
