Here are Allen Institute resources to help you understand the fundamentals of cell types and the research methods used to study cell types; including Patch-Seq, taxonomies, UMAPs, and more. These sections are designed for those who are unfamilar with cell type topics to help introduce them to the concepts.
Cells within a type exhibit similar structure and function that are distinct from cells in other types.
1. Learn from our Executive Vice President & Director of Brain Science, Hongkui Zeng, on the overview of cell types from the roots in evolution & development to the approaches in how to characterize, while also providing a roadmap for the future.
2. Cell Types 101 Webinar focuses on an introduction to the study of cell types! It covers evolving cell type definitions, cell types across species, the types of data used to define cell types, and the importance of having standard definitions for cell types.
The study of RNA expression (the transcriptome) and how it differs between cells / tissues / conditions.
This webinar is tutorial on Allen Cell Types Database. Starting at 4:13, we give an overview of single cell or nucleus transcriptomics. (Note: Webinar is from 2021; the taxonomies presented in the webinar are not the latest taxonomies from the Institute, as newer taxonomies have been created since 2021.)
This guide book describes how 10x single cell sequencing works with easy-to-understand language and graphics.
A cell type taxonomy is a specific analysis organizing cells into groups (or types), applied to a specific set of data, and saved in a standard format. Cell types are annotated with data-driven and historical information about their characteristics.
1. This user-friendly tutorial goes step by step on how cell type taxonomies are created, with linking to data from Allen Cell Types Database in the end. This is a great web-interface that is perfect for students to experts to begin exploring what a taxonomy is.
Explore the Interative Walkthrough
Related tool: Allen Cell Types Database
Related Publication (Tasic et al 2016)
2. 'What is a taxonomy?' webinar is focused on the systematic classification of cell types and their hierarchical relationships. Much like species taxonomy (family, genus, species, etc.), researchers at the Allen Institute and their collaborators are working to create a standard taxonomy for cell types.
Uniform Manifold Approximation and Projections (or 'UMAPs') are helpful ways of displaying many types of data and are often referred to as one type of dimensionality reduction tool.
A UMAP is a common way to visualize cell types taxonomies. Learn how to interpret and analyze these graphs in this user guide.
Patch-Seq is modified version of Patch-Clamp, with the additional steps of extracting the nucleus to obtain transcriptomics and preserving the cell body to obtain morphology.
1. Patch-Seq was developed around late 2010s, with Allen Institute helping to optimize the technique. Here is a 2016 Allen Institute team talk giving an overview of Patch-Seq.
Watch the Team Talk
See other Patch-seq resources and publications
2. This webinar from 2024 gives an overview of what Patch-Seq is and how that data is used in the Cell Type Knowledge Explorer tool.
Watch the webinar
Explore motor cortex cell types in the Cell Type Knowledge Explorer
Discover all pages in this series:
This third section "Putting it all together" is a key to link research focus to related scientific tool to primary paper to taxonomy used.
This second section "How to..." lists more technical resources such as tutorials, protocols, use cases, and more.
Learn about Rna Seq Process Controls with comprehensive guides and examples from Allen Institute for Brain Science.
