image representing the current explore topic

Cell Types Support: tutorials, protocols, and more

This support page is a catalog of Allen Institute's resources to help better understand cell types. The first section is "What is..." lists introductory information on cell type topics. The second section is "How to..." lists more technical resources such as tutorials, protocols, use cases, and more. The third section is "Putting it all together" is a key to link research focus to related scientific tool to primary paper to taxonomy used.

 

Each resource has additional information such as that resource's citation, any related papers,  and/or related scientific tools. Click on the button to view to the listed resource.

 

Page Contents

What is...: What is a cell type? | What is transcriptomics? | What is a taxonomy? | What is a UMAP? | What is Patch-Seq?
How to..: How to understand cell type nomenclature | How to replicate our Patch-Seq | How to replicate our RNA-Seq | How to use Cell Type Knowledge Explorer | How to use ABC Atlas | How to use MapMyCells

Putting it altogether:  Mouse (Healthy: Whole Brain, Visual & Motor Cortex, Hippocampus) | Human (Healthy: Whole Brain, Motor Cortex, MTG) | Human (Alzhiemer's: MTG & DLPFC) | Marmoset (Motor Cortex)


What is...?

Introductory resources

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.

 

What is a cell type?

Cells within a type exhibit similar structure and function that are distinct from cells in other types.

What is a cell type and how to define it? Review Paper

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.

Type of resource

Review Paper

Citation

Zeng H. What is a cell type and how to define it? Cell. 2022 Jul 21;185(15):2739-2755

 

Cell Types 101 Webinar

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.

Type of resource

Webinar

Citation

Allen Institute. (2024, Feb). What is a taxonomy? [Video]. YouTube. https://www.youtube.com/watch?v=2D89hm3cWIQ

 

What is transcriptomics?

The study of RNA expression (the transcriptome) and how it differs between cells/tissues/conditions.

Single cell or nucleus transcriptomics Webinar

This webinar is tutorial on Allen Cell Types Database. Starting at 4:13, we give an overview of single cell or nuclues 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. 

Type of resource

Webinar

Citation

Allen Institute (2021, March). Open for (neuro)science tutorials: Allen Cell Types Database – Transcriptomics. Youtube. https://www.youtube.com/live/rNX1LopFFLA

 

What is a (cell type) taxonomy?

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.

Taxonomy Walkthrough

User-friendly tutorial that 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.

Type of resource

Interactive walkthrough

Releated Tool

Allen Cell Types Database

Related Paper

Tasic, B., et al. (2016) Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.

Citation

Allen Institute. (2016). A Cellular Taxonomy of the Mouse Visual Cortex. http://casestudies.brain-map.org/celltax

 

What is a taxonomy? Webinar

'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.

Type of resource

Webinar

Citation

Allen Institute. (2024, Feb). What is a taxonomy? [Video]. YouTube. https://www.youtube.com/watch?v=2D89hm3cWIQ

 

What is a UMAP?

Uniform Manifold Approximation and Projection (UMAP). UMAPs are helpful ways of displaying many types of data and are often referred to as one type of dimensionality reduction tool.

UMAP Guide

UMAP is a common way to visualize cell types taxonomies. Learn how to interpret and analyze these graphs.

Type of resource

Guide

Citation

Meuler, M. (2023). What is a UMAP?. https://alleninstitute.org/resource/what-is-a-umap/

 

What is Patch-Seq?

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.

Patch-Seq Team Talk

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.

Type of resource

Team Talk

Citation

Allen Institute. (2016, December). 2016 | Showcase | Team Talk | Patch-Seq Data [Video]. YouTube. https://www.youtube.com/watch?v=QxTJeSao8Uo

 

Patch-Seq & Cell Type Knowledge Explorer Overview Webinar

This webinar from 2024 gives an focus on overview of what Patch-Seq is, and how that data is used in the tool, Cell Type Knowledge Explorer.

Type of resource

Webinar

Related Tool

Cell Type Knowledge Explorer

Citation

Allen Institute. (2024, March). Techniques behind Cell Type Knowledge Explorer? [Video]. YouTube. https://www.youtube.com/watch?v=vLHRWxg_-RA

 

 


How to...

Technical Protocols, Guides, Useful Supplemental Information

These are Allen Institute resources to explain how to use our datasets, replicate our experiments with protocols, and links to tables with important metadata and features definitions. These sections are designed for scientists who are interested in more techincal support in their cell types reserach.

 

How to understand cell type nomenclature

Common Cell Type Nomeclature Guide

Understand the framework for developing nomenclatures—called the Common Cell Type Nomenclature, or CCN.

Type of resource

Guide

Related Paper

Miller, J. A., et al. (2020) Common cell type nomenclature for the mammalian brain eLife 9:e59928

 

How to replicate our Patch-Seq protocols and analysis

Patch-Seq Adoption GitHub

Adopting the Patch-seq technique in a lab can be daunting. To make adoption as simple as possible, this GitHub provides a starting point for labs interested in using the Patch-seq technique or refining their existing technique. Specifically, this resource consists of three components: (1) a step-by-step optimized Patch-seq protocol (2) the Multichannel Igor Electrophysiology Suite (MIES) software package and (3) an R library that uses a modified workflow. 

Type of resource

GitHub Protocol Hub

Related Paper

Lee, B. R., et al. (2021) Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

Citation

Allen Institute Patch-seq documents and tools. (2021). https://github.com/AllenInstitute/patchseqtools

 

Protocol: Electrophysiology recording and extraction
From our electrophysiology team, this is detailed protocol to obtain electrophysiological recordings and cellular contents from neurons in postnatal mouse and/or human brain slices.

Type of resource

Protocol

Used in Related Tools

Allen Cell Types Database
Mouse PatchSeq VISp

Used in Datasets

Mammalian PatchSeq Datasets

Related Paper

Lee, B. R., et al. (2021) Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

Citation

Lee, B., Hadley, K., Allen Institute for Brain Science (2021). Patch-Seq Recording and Extraction Detailed Protocol V.2

 

Automatic computing for electrophysiological cell features
IPFX is a Python package for computing intrinsic cell features from electrophysiology data. That can perform cell data quality control (e.g. resting potential stability), detect action potentials and their features (e.g. threshold time and voltage), calculate features of spike trains (e.g., adaptation index), and calculate stimulus-specific cell features

Type of resource

GitHub Repository

Used in Datasets

Mammalian PatchSeq Datasets

Citation

IPFX (2022). https://github.com/AllenInstitute/ipfx

 

Protocol, Software, Analysis: Reconstruct neuron morphology
Here is your one-stop shop for the Allen Institute’s free, open-source neuron reconstruction software, protocols, and analysis scripts for generating and analyzing image-based, quantitative, 3D morphologies for your own research.

Type of resource

Protocol, Software, Analysis

Used in Related Tools

Allen Cell Types Database
Mouse PatchSeq VISp

Used in Datasets

Mammalian PatchSeq Datasets

Citation

Allen Institute (2023). How To Reconstruct Neurons in 3D. https://portal.brain-map.org/explore/toolkit/morpho-reconstruction/vaa3d-mozak

 

Takara SMARTer V4
Protocol to generate full-length cDNA from single cells, or nuclei, using Takara SMARTer V4.

Type of resource

Protocol

Used in Related Tools

Allen Cell Types Database
Mouse PatchSeq VISp

Used in Datasets

Mammalian PatchSeq Datasets

Citation

Allen Institute 2023. SMARTerV4 (1x) Amplification for single-cell or single-nuclei RNASeq Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.261geopdjl47/v2 Version created by Allen Institute

 

Electrophsyiology & Morphology Features Definition

The electrophysiology and morphology feature definitions are used for all our Patch-Seq datasets. This is from “NIHMS1691616-supplement-Supplementary_Figures” in Gouwens, Sorensen, Berg, et al. 2019, starts at page 73 for electrophysiology and page 75 for morphology.

Type of resource

Supplemental Table

Related Tools

Allen Cell Types Database
Mouse PatchSeq VISp
Cell Type Knowledge Explorer

Related Datasets

Mammalian PatchSeq Datasets

Citation

Gouwens, N.W., Sorensen, S.A., Berg, J. et al. (2019). Classification of electrophysiological and morphological neuron types in the mouse visual cortex

 

How to replicate our RNA-Seq laboratory protocols

SOPs: RNA-Seq mouse whole cortex & hippocampus

SOPs: RNA-seq human multiple cortex areas

This page includes protocols for SMART-Seq and Nextera XT, FACs, and tissue preparation and analysis & clustering links.

Type of resource

Protocols, Analysis

Citation

See protocols.io "Metadata" for individual citations

 

RNA-Seq controls

To monitor for a consistent, high-quality sampling of single-cell and single-nucleus RNA-Seq data, we have controls used in each application sample. These controls for mouse and human data are available to download for you to use in your own experiments.

Type of resource

Supportive Data

Citation

See protocols.io "Metadata" for individual citations

 

How to use Cell Type Knowledge Explorer Explore Cell Type Knowledge Explorer

Scientific tool for entry point for exploration of individual cell type taxonomies for human, marmoset and mouse primary motor cortex.

Video Tutorial Written Tutorial

Learn from the scientists behind our Cell Types Knowledge Explorer about why it is made, key findings, and a walkthrough of the tool itself.

Type of resource

Tutorial

Related Tool

Cell Type Knowledge Explorer

Related Papers

Patch-Seq (Mouse): Scala, F., et al. (2021). Phenotypic variation of transcriptomic cell types in mouse motor cortex. Nature. DOI: 0.1038/s41586-020-2907-3
Cross-Species: Bakken, T. E., Jorstad, N. L., Hu, Q., et al. (2021). Comparative cellular analysis of motor cortex in human, marmoset and mouse. DOI 10.1038/s41586-021-03465-8
Transcriptomics & Epigenomics: Yao, Z. et al. (2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature, 598(7879):103-110. DOI 0.1038/s41586-021-03500-8

Citation

Video: Allen Institute. (2023, April). BICAN presents: Cell Types Knowledge Explorer tutorial [Video]. YouTube. https://www.youtube.com/watch?v=xJRBQzZLX4s

 

Use Case Example: Experimental Design

These use cases were designed to show researchers how to use the mouse data in the Cell Type Knowledge Explorer for their own research questions. The case titled “Experimental Design” shows how the Cell Type Knowledge Explorer can be used to guide research questions.

Type of resource

Guide

Related Tool

Cell Type Knowledge Explorer, Mouse

 

Replicate our data visualization

Python code for you to your own generate data visualizations that was used in the Cell Type Knowledge Explorer.

Type of resource

GitHub

Related Tool

Cell Type Knowledge Explorer

Citation

CTKE Viz (2022). https://github.com/AllenInstitute/CTKE_viz

 

How to use ABC Atlas Explore ABC Atlas

The Allen Brain Cell (ABC) Atlas provides a platform for visualizing multimodal single cell data across the mammalian brain and aims to empower researchers to explore and analyze multiple whole-brain datasets simultaneously.
User Guide

From our product managers of ABC Atlas, here is a user guide to help you navigate all the features of ABC Atlas.

Type of resource

User Guide

Related Tool

ABC Atlas

Related Papers

Mouse (Spatial & Non-Spatial Transcriptomics, Coronal): Yao et al. (2023) A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. DOI 10.1038/s41586-023-06812-z.
Mouse (Spatial Transcriptomics, Coronal & Sagittal): Zhang, M., Pan, X., Jung, W. et al. (2023). Molecularly defined and spatially resolved cell atlas of the whole mouse brain. DOI 10.1038/s41586-023-06808-9
Whole Human: Siletti, K. Hodge, R., et al. (2023). Transcriptomic diversity of cell types across the adult human brain. DOI: 10.1126/science.add7046
Alzheimer’s Disease, Human (SEA-AD): [Pre-print] Gabitto, M. I., Travaglini, K. J., et. al. (2023). Integrated multimodal cell atlas of Alzheimer’s disease

 

Use Case Examples of ABC Atlas – Experimental Design

Use Case Examples of ABC Atlas – Scientific Knowledge

Use Case Examples of ABC Atlas – Experimental Design with Coding
These use cases were designed to show researchers how to use the Whole Human Brain data in the ABC Atlas for their own research questions. The two use cases titled “Experimental Design” show how the ABC Atlas can be used to guide research questions, while the use case titled “Scientific Knowledge” shows how the ABC Atlas can be used studying and/or writing a literature review. The “coding” in the third use case shows users how to access the raw data for the Whole Human Brain using Jupyter notebooks.

Type of resource

Use Case

Related Tool

ABC Atlas, Whole Human Brain

 

Whole Mouse Brain Paper Package Highlights Webinar
Learn from the scientists behind the new collection of studies from the BRAIN Initiative Cell Atlas Network (biccn.org) and published in Nature on Dec 14, 2023

Type of resource

Webinar

Related Tool

ABC Atlas, Whole Mouse Brain

Related Paper

Brain Initiative Cell Census Network 2.0, Nature 2023 Paper Package

Citation

Allen Institute. (2024, February). Whole Mouse Brain Atlas Publication Package Highlights (Feb 1, 2024) [Video]. YouTube. https://www.youtube.com/watch?v=l5NHSLk6O-A

 

Whole Mouse Brain, Spatial Gene Panel List
List of the 500 Gene panel used in the whole brain mouse. This is from the supplemental table 6 in Yao, et al. 2023

Type of resource

Supplemental

Related Tool

ABC Atlas, Whole Mouse Brain, Spatial

 

Whole Mouse Brain, Annotation Table
Detailed information for each cluster, neurotransmitter information, overall marker genes, main dissection region, and more. This is from the supplemental table 7 in Yao, et al. 2023.

Type of resource

Supplemental

Related Tool

ABC Atlas, Whole Mouse Brain, Spatial

 

ABC Atlas Update Notes
See all the updates & patches to ABC Atlas.

Type of resource

Update Notes

Related Tool

ABC Atlas

 

How to use MapMyCells Explore MapMyCells

MapMyCells allows you discover what cell types your transcriptomics and spatial data corresponds with by comparing you data to our massive, high-quality reference datasets.

MapMyCells Webinar

Learn from one of our scientists behind MapMyCells on how to use it, what type of data it accepts, what taxonomies are built of fit, which algorithms to select, and peek under the hood on how it works.

Type of resource

Webinar

Related Tool

MapMyCells

Citation

Allen Institute. (2024, April). What is your cell type: MapMyCells [Video]. YouTube. https://www.youtube.com/watch?v=JjzRMF3lyK0

 

Input creation, file requirements, and limits

MapMyCells needs cell by gene matrix where rows are “cells” and columns are “genes”, which need to be in file format h5ad. This guide provides more details about your input file limits, how to create h5ad from csv, example h5ad files and more!

Type of resource

Guide

Related Tool

MapMyCells

 

Cell type references, algorithms, and output files
Unsure what algorithm or taxonomy to select in MapMyCells? This guide is for you.

Type of resource

Guide

Related Tool

MapMyCells

 

Workbook to run MapMyCells independently
The online version of MapMyCells will provide accurate cell type assignments for user-inputted data in most cases. However, there are some situations when using the direct scripts may be more appropriate: (1) if the reference taxonomy you are interested in is not one currently included in MapMyCells, (2) if the data set you have is quite large, (3) if you'd like to include these algorithms as part of an analysis pipeline, or (4) if you need to select a different set of genes for mapping (e.g., for mapping MERFISH data).

Type of resource

Workbook Guide

Related Tool

MapMyCells

 

BICCN and BICAN

Guide to BICAN Ecosystems

Most of these resources are part of the Brain Initiative Cell Census Network (BICCN) and/or Brain Initiative Cell Atlas Network (BICAN). The Allen Institute serves as the coordinating member of this network.

Type of resource

Review Paper

Citation

Hawrylycz, M., et al. (2023). A guide to the BRAIN Initiative Cell Census Network data ecosystem

 

 


Putting it all together

The associated tool::paper::taxonomy::research focus

This table links the research topic (species, brain area of interest, and technique) to the related tool, the related dataset, the related paper, and the related taxonomy.

 

Research model, area of interest

TECHNIQUE

Related Tool

Project Summary

Related Paper

Related Taxonomy

Mouse, Whole Brain

Spatial transcriptomics & single cell RNA-Seq

ABC Atlas (Spatial & non-spatial, coronal)

Whole Mouse Brain Transcriptomic Cell Type Atlas

Yao et al. (2023) A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. DOI 10.1038/s41586-023-06812-z.

Whole adult mouse brain taxonomy of cell types

Mouse, Whole Brain

Spatial transcriptomics

ABC Atlas (Spatial, coronal & sagittal)

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

Zhang et al. (2023) Molecularly defined and spatially resolved cell atlas of the whole mouse brain. DOI 10.1038/s41586-023-06808-9

Whole adult mouse brain taxonomy of cell types

Mouse, Whole Cortex & Hippocampus

Single cell RNA-Seq (SMART-Seq and 10x)

Transcriptomic Explorer (SMART-Seq)

Transcriptomic Explorer (10x)

Mouse - Whole Cortex & Hippocampus - SMART-seq

Mouse - Whole Cortex & Hippocampus - 10x

Yao, Z., et al. (2021). A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. DOI 10.1016/j.cell.2021.04.021
 

Cell types taxonomy (2021)

Cell types taxonomy (2021) viewer

Mouse, Primary Visual Cortex & Anterior Lateral Motor Cortex

Single cell RNA-Seq

RNA-Seq Mouse Data Navigator

Transcriptomic cell types in the mouse brain: SMART-seq cells

Tasic, B., et al. (2018). Shared and distinct transcriptomic cell types across neocortical areas. DOI 10.1038/s41586-018-0654-5

Taxonomy embedded in VISp and ALM

Mouse, Primary Motor Cortex

Patch-Seq

Cell Type Knowledge Explorer

Patch-seq of mouse motor cortex: transcriptomics

Scala, F., et al. (2021). Phenotypic variation of transcriptomic cell types in mouse motor cortex. DOI 10.1038/s41586-020-2907-3

Taxonomy embedded in the download files for the "10x Chromium v3 (Broad)" dataset

Mouse, Primary Motor Cortex

Single cell RNA-Seq

Cell Type Knowledge Explorer

Transcriptomic cell types in the mouse brain: 10x nuclei

Yao, Z. et al. (2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. DOI 10.1038/s41586-021-03500-8

Taxonomy embedded in the download files for the first seven datasets

Mouse, Primary Visual Cortex

Patch-Seq

Mouse PatchSeq VIS

Neurons in Mouse Primary Visual Cortex

Gouwens, N. W., et al. (2020). Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. DOI 10.1016/j.cell.2020.09.057

Subset of taxonomy embedded in VISp download; includes all GABAergic neurons and VISp glutamatergic neurons.

Mouse, (majority) Visual Cortex

Patch-Clamp

Allen Cell Types Database

N/A

Gouwens, N. W., et al. (2019) Classification of electrophysiological and morphological neuron types in the mouse visual cortex. DOI 10.1038/s41593-019-0417-0

No associated transcriptomic taxonomy

Human, Whole Brain

Single nucleus RNA-Seq

ABC Atlas

Transcriptomic diversity of cell types in adult human brain

Siletti, K., Hodge, R., et al. (2023) Transcriptomic diversity of cell types across the adult human brain. DOI:10.1126/science.add7046

Human whole brain

Human, Multiple Cortical Areas

Single nucleus RNA-Seq

Transcriptomic Explorer

Human Multiple Cortical Areas - SMART-seq

*some of the data  
Jorstad, N. L., et al. (2023) Transcriptomic cytoarchitecture reveals principles of human neocortex organization. DOI:10.1126/science.adf6812

Taxonomy for transcriptomic explorer

Taxonomy from paper (Newer Data) 

Human, Primary Motor Cortex

Single nucleus RNA-Seq

Cell Type Knowledge Explorer


Transcriptomic Explorer

Transcriptomic characterization of cell types in human M1 using droplet-based single nucleus RNA sequencing

Bakken, T. E., Jorstad, N. L., Hu, Q., et al. (2021). Comparative cellular analysis of motor cortex in human, marmoset and mouse. DOI 10.1038/s41586-021-03465-8

Human M1 10x

Human, Middle Temporal Gyrus
 

Single nucleus RNA-Seq

RNA-Seq Navigator

Transcriptomic characterization of cell types in human M1 using droplet-based single nucleus RNA sequencing

Hodge, R. D., Bakken, T. E., et al. (2019). Conserved cell types with divergent features in human versus mouse cortex. DOI: 0.1038/s41586-019-1506-7.

Human MTG SMART-seq

Human, Middle Temporal Gyrus, Alzhiemer's Disease

Spatial Transcriptomics

ABC Atlas

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) - Spatial transcriptomics - MERFISH

[Pre-print] Gabitto, M. I., Travaglini, K. J., et. al. (2023). Integrated multimodal cell atlas of Alzheimer’s disease

Mapped to this expanded aged/AD donor taxonomy

Human, Middle Temporal Gyrus, Alzhiemer's Disease

Single nucleus RNA-Seq

ABC Atlas

 

Transcriptomic Explorer

Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) - 10x single nucleus RNAseq

[Pre-print] Gabitto, M. I., Travaglini, K. J., et. al. (2023). Integrated multimodal cell atlas of Alzheimer’s disease

Adult donor taxonomy

Marmoset, Primary Motor Cortex

Single nucleus RNA-Seq

Cell Type Knowledge Explorer

A Molecular and Cellular Atlas of the Marmoset Brain - Single nucleus sequencing

Bakken, T. E., Jorstad, N. L., Hu, Q., et al. (2021). Comparative cellular analysis of motor cortex in human, marmoset and mouse. DOI 10.1038/s41586-021-03465-8

Embedded in the metadata file on NeMO

 

This page was last updated May 2024.