Brain Initiative Cell Census Network 2.0

Generating a multimodal cell census and atlas of a complete mammalian brain through collaborative data collection, tool development and analysis.

As large-scale neuroscience projects start to yield results, sharing data standards will become increasingly important.

In a huge collaborative effort, millions of cells in the mouse brain have been mapped in detail. Two scientists examine the resulting wealth of insights into gene regulation in brain cells, neuronal connections and how our own brains evolved.

 A transcriptomic cell-type atlas of the whole adult mouse brain with ~5,300 clusters built from single-cell and spatial transcriptomic datasets with more than eight million cells reveals remarkable cell type diversity across the brain and unique cell type characteristics of different brain regions. 

A comprehensive cell atlas of the whole mouse brain with high molecular and spatial resolution is generated.

To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq, a recently developed spatial transcriptomics method with near-cellular resolution, across the entire mouse brain.

Methylome-based clustering and cross-modality integration with companion datasets from the BRAIN Initiative Cell Census Network enabled the construction of a 3D multi-omic genome atlas of the adult mouse brain featuring thousands of cell-type-specific profiles.

An atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain unravels the transcriptional regulatory programs that drive the heterogeneity and complexity of brain structure and function.

This study uses epi-retro-seq to link single-cell epigenomes and cell types to long-distance projections for neurons dissected from different regions projecting to different targets across the whole mouse brain.

In this study, the authors develop a comprehensive taxonomy of brain-wide SPNs, identifying several novel subsets via their transcriptional signatures.

In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.

A single-cell multiomics analysis of over 200,000 cells of the primary motor cortex of human, macaque, marmoset and mouse shows that divergence of transcription factor expression corresponds to species-specific epigenome landscapes, and conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome.

Single-cell and single-nucleus transcriptomic analysis of retina from 17 vertebrate species shows high conservation of retinal cell types and suggests that midget retinal ganglion cells in primates evolved from orthologous cells in ancestral mammals.

RNA alternative splicing is involved in determining cell identity, but a comprehensive molecular map is missing. Here, the authors provide a human and mouse brain atlas of transcript isoforms linking them to cellular identity, brain regions and development stages.