Cell Census of the Primary Motor Cortex

A multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) has been achieved as the initial product of the BRAIN Initiative Cell Census Network (BICCN). Coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. These results represent a major milestone in the effort to create a catalog or census of all brain cell types and advance the collective knowledge and understanding of brain cell type organization, and this site provides a guide to the flagship and core companion papers for the work.

This site provides a guide to the flagship and core companion papers for the work.

Major highlights of the study reveal:

A unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps.
Cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human.
Cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes.
In situ single-cell transcriptomics provides a spatially resolved cell type atlas of the motor cortex.
Integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types.

An extensive genetic toolset was also developed for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, the results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular, genetic and spatial information with multi-faceted phenotypic properties.

Explore the BICCN Data Inventory

This includes quick links to BICCN Data Catalog with filtered searches.

By Species

HUMAN

MARMOSET

MOUSE

By Data Modality

anatomy and connectivity

electrophysiology

spatial transcricptomics

cell morphology

transcriptomics and epigenomics

population imaging

Explore Tools for the Cell Census of the Primary Motor Cortex

Read about the visualization tools and data processing pipelines that supported the Cell Census of the Primary Motor Cortex.

Explore the Collection of Papers

The Flagship paper and Companion papers are listed below with links to the published article DOIs and to visualization tools that support access to data highlighted in those papers.

FLAGSHIP PAPER

Explore data at:

A multimodal cell census and atlas of the mammalian primary motor cortex.

BRAIN Initiative Cell Census Network (BICCN; Edward M. Callaway, Hong-Wei Dong, Joseph R. Ecker, Mike Hawrylycz, Z. Josh Huang, Ed S. Lein, John Ngai, Pavel Osten, Bing Ren, Andreas S. Tolias, Owen White, Hongkui Zeng, Xiaowei Zhuang)

NeMO Analytics: Flagship Patchseq‍

‍NeMO Analytics: Merfish MOp
‍‍NeMO Analytics: Flagship MOp genomics

COMPANION PAPERS

Explore data at:

A transcriptomic and epigenomic cell atlas of mouse primary motor cortex.

Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer,...,Hongkui Zeng, Eran Mukamel.

cellxgene‍
‍NeMO Analytics: BICCN Mini-Atlas (Integrated)
‍‍NeMO Analytics: BICCN Mini-Atlas (Transcript)‍
‍NeMO Analytics: MOp Mouse Epigenetic‍
‍Azimuth

‍UCSD Brainome‍
Single Cell Portal‍
‍Single Cell Portal‍
‍Single Cell Portal
‍‍Single Cell Portal

Comparative cellular analysis of motor cortex in human, marmoset, and mouse.

Trygve Bakken,...,Ed S. Lein.

cellxgene‍
NeMO Analytics: Motor cortex cross species
‍‍NeMO Analytics: Motor cortex merged species
‍‍NeMO Analytics: Cross-species ATAC

‍cytosplore
‍‍Azimuth‍
‍Transcriptomics Explorer

DNA methylation atlas of the mouse brain at single-cell resolution.

Hanqing Liu, Jingtian Zhou...,Joseph R. Ecker.

Brain Cell Methylation Viewer

An atlas of gene regulatory elements in adult mouse cerebrum.

Yang E. Li, Sebastian Preissl,...,Bing Ren.

cellxgene‍
‍Catlas

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH.

Meng Zhang,...,Xiaowei Zhuang.

cellxgene

Phenotypic variation of transcriptomic cell types in mouse motor cortex.

Federico Scala, Dmitry Kobak,...,Philipp Berens, Andreas S. Tolias.

Neuromorpho.org

Human neocortical expansion involves glutamatergic neuron diversification.

Jim Berg, Staci A. Sorensen, Jonathan T. Ting, Jeremy A. Miller,...,Ed S. Lein.

Neuromorpho.org

Epigenomic diversity of cortical projection neurons in the mouse brain.

Zhuzhu Zhang, Jingtian Zhou,...,Joseph R. Ecker, Edward M. Callaway.

Cellular anatomy of the mouse primary motor cortex.

Rodrigo Muñoz-Castañeda, Brian Zingg, Katherine S. Matho, Xiaoyin Chen, Quanxin Wang,...,Hong-Wei Dong, Julie A. Harris, Pavel Osten, Z Josh Huang, Giorgio A. Ascoli.

Neuromorpho.org

Morphological diversity of single neurons in molecularly defined cell types.

Hanchuan Peng, Peng Xie, Lijuan Liu,...,Hanchuan Peng, Hongkui Zeng.

Neuromorpho.org

Genetic dissection of the glutamatergic neuron system in cerebral cortex.

Katherine Matho,..., Z. Josh Huang.

The mouse cortico-basal ganglia–thalamic network.

N N Foster,...,Hong-Wei Dong.

Isoform cell type specificity in the mouse primary motor cortex.

A Sina Booeshaghi,...,Lior Pachter.

An atlas of cortical arealization identifies dynamic molecular signatures.

Aparna Bhaduri, Carmen Sandoval-Espinosa,...,Arnold Kriegstein.

Single-cell epigenomics reveals mechanisms of human cortical development.

Ryan Ziffra,...,Tomasz Nowakowski.

A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types.

Velina Kozareva, Caroline Martin,...,Evan Macosko.

Molecular logic of cellular diversification in the mouse cerebral cortex.

Daniela J. Di Bella,...,Aviv Regev, Paola Arlotta.

Single Cell Portal
‍‍Gene Expression Omnibus