Resources for "A Multimodal Cell Census and Atlas of the Mammalian Primary Motor Cortex", 2021

We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by 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. The study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, 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. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. This page provides a guide to access accessing data and tools associated with this work

A series of companion studies supported the findings in this manuscript.

• An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types, Yao et al., 2020
• Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse, Bakken et al., 2020
• Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics, Zhang et al, 2020
• Phenotypic variation of transcriptomic cell types in mouse motor cortex, Scala et al, 2020
• Cellular Anatomy of the Mouse Primary Motor Cortex, Munoz-Casteneda, 2020
• Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex, Matho et al,2020
• DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution, Liu et al., 2020
• Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain, Zhang et al., 2020
• An atlas of gene regulatory elements in Adult Mouse Cerebrum, Li et al, 2020
• Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons, Berg et al,2020
• Brain-wide single neuron reconstruction reveals morphological diversity in molecularly defined striatal, thalamic, cortical and claustral neuron types, Peng et al,2020

Data and supporting codes related to analyses in figures.

1. Figure 1: Summary of experimental and computational approaches taken and as well as community resources generated by BICCN.
2. Figure 2: MOp consensus cell type taxonomy.
3. Figure 3: In situ cell-type identification, spatial mapping and projection mapping of individual cells in the MOp by MERFISH
4. Figure 4: Correspondence between transcriptomic and morpho-electrical properties of mouse MOp neurons by Patch-seq, and cross-species comparison of L5 ET neurons.
5. Figure 5: Epi-Retro-Seq links molecular cell types with distal projection targets.
6. Figure 6: Genetic tools for targeting cortical glutamatergic projection neuron types.
7. Figure 7: Global wiring diagram and anatomical characterization of MOp-ul neuron types.
8. Figure 8: Existence of L4 excitatory neurons in MOp.
9. Figure 9: Two distinct L5 ET projection neuron types in MOp.
10. Figure 10: An integrated multimodal census and atlas of cell types in the primary motor cortex of mouse, marmoset and human.

All primary data is accessible through the Brain Cell Data Center (BCDC) and data archives.

• Brain Cell Data Center (BCDC), www.biccn.org
• Neuroscience Multi-omic Data Archive (NeMO), NeMO, Transcriptomics and epigenomics data in this study
• Brain Image Library, BIL, Imaging data used in this study
• Distributed Archives for Neurophysiology Data Integration, DANDI

The following papers are referenced techniques other than those in the companion papers.

• Shared and distinct transcriptomic cell types across neocortical areas, Tasic et al., 2018
• Conserved cell types with divergent features in human versus mouse cortex, Hodge et al., 2019
• Innovations present in the primate interneuron repertoire, Krienen et al., 2020
• A transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell types, Kozareva et al., 2020
• A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation, Yao et al., 2020

• Robust single-cell DNA methylome profiling with snmC-seq2, Luo et al., 2018
• Spatiotemporal DNA methylome dynamics of the developing mouse fetus, He et al., 2018

• Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation, Preissl et al., 2018

• High-throughput sequencing of the transcriptome and chromatin accessibility in the same cel, Chen et al., 2019

• RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells, Chen et al., 2015
• Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region, Moffitt et al., 2019

• Comprehensive integration of single cell data, Stuart et al., 2019
• Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity, Welch et al., 2019
• Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Crow et al., 2018

• Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq, Cadwell et al., 2016
• Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq, Cadwell et al., 2017

• High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level, Gong et al., 2016
• Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain, Winnubst et al. 2019

• Neural networks of the mouse cortex, Zingg et al., 2014
• AAV-Mediated Anterograde Transsynaptic Tagging: Mapping Corticocollicular Input-Defined Neural Pathways for Defense Behaviors, Zingg et al., 2017

• Genetic dissection of glutamatergic neuron subpopulations and developmental trajectories in the cerebral cortex, Matho et al., 2020

Panel 2a

Panels 2b-2g:

• 10x V3 macaque
• 10x V3 human (10X159-1 through 10x160-8)
• 10x V3 marmoset (bi005_m1, bi006_m1)
• 10x V3 mouse Broad data (files with prefix pBICCNsMMrMOp)

Panel 2a

Panel 2b: Dendrogram reproduced from companion paper (Bakken et al. 2020)

Panel 2c

Panels 2d, 2e

Panels 2f, 2g: Reproduced from companion paper (Bakken et al. 2020)

Panel 2h

Panel 2i: Custom UCSC browser of all M1 tracks

Panel 2j: Browser

Extended Data Figure 1

MERFISH raw data and processed data

MERFISH data processing pipeline

Panel 3b

Panel a:

• Patch-seq mouse transcriptomic data in FASTQ format
• Biccn/grant/zeng/zeng/transcriptome

Panels b-g:

• Morphological reconstructions in SWC format
• Electrophysiological traces in NWB format

Panel h:

• 10x V3 macaque
• 10x V3 human (10X159-1 through 10x160-8)
• 10x V3 marmoset (bi005_m1, bi006_m1)
• 10x V3 mouse Broad data (files with prefix pBICCNsMMrMOp) Panels i-k:
• Electrophophysiology in NWB format
• Morphological reconstructions in SWC format

Panel h:

• 10x 4 species integration
• Code

Panels a-g:

• Code

Epi-Retro-Seq raw data

Gene Expression Omnibus data

Code

Panel c

Panels d-k

Panel j

Panel c

Panels d-i

panel c https://github.com/AllenInstitute/MOp_anatomy_rendering code to reproduce rendering of registered data in 3D

Panels 8a,c,e

Panel 8b

Panel 9d

Panel 9e

snATAC-seq Utilites

snATAC-seq Utilites

Extended data figure 3