Paper Review:
A detailed atlas mapping genes, cell types, and their spatial organization throughout an entire mammalian brain is essential for unraveling brain function. Yet, a complete whole-brain atlas for the mouse with both single-cell and high spatial resolution remains unavailable.
A new research, titled "Single-cell spatial transcriptomic atlas of the whole mouse brain", published in Neuron, created a single-cell resolution map of the entire mouse brain using Stereo-seq– high resolution spatial whole transcriptome profiling technology and single-nucleus RNA sequencing (snRNA-seq). This atlas, encompassing over 4 million spatially resolved cells and 29,655 genes (covering 95.5% of annotated protein-coding and non-coding genes), represents a monumental achievement.
The atlas identifies coding genes and long non-coding RNAs (lncRNAs) enriched in specific brain regions and subregions, highlighting their potential roles in localized brain functions and development. By analyzing gene expression patterns, the researchers delineated 148 brain regions, achieving high consistency with the Allen Brain Atlas Common Coordinate Framework (CCFv3). Notably, they identified finer subdivisions in areas like the caudate putamen and nucleus accumbens, revealing previously unrecognized structural details. The study examined mouse brains from embryonic to adult stages, uncovering the dynamics of 573 transcription factor (TF) regulons in the adult brain and 998 across seven developmental stages. These regulons, which control gene expression, vary in activity across regions like the cortex, striatum, thalamus, and cerebellum, providing insights into how genetic programs shape brain development.
Stereo-seq in the paper enables the creation of a detailed single-cell spatial transcriptomic atlas of the mouse brain. Its ability to map gene expression with high resolution and integrate with snRNA-seq has provided a wealth of insights into brain architecture, development, and disease. The study's dataset is available online (https://doi.org/10.12412/BSDC.1699433096.20001), allowing scientists worldwide to explore and build on this research, potentially leading to new discoveries in neuroscience.
Find out more about the research: https://www.cell.com/neuron/abstract/S0896-6273(25)00133-3
About STOmics Stereo-seq:
STOmics offers the most advanced spatiotemporal multi-omics technology, enabling unbiased discovery to answer biological questions in scientific research and clinical applications. Currently, we offer spatial transcriptomics solutions, including Stereo-seq v1.3 for fresh frozen samples, Stereo-seq OMNI for FFPE samples, Stereo-seq Large Chip Designs (LCD) for centimeter-level fresh frozen samples (now up to 2cm x 3cm), and a spatial multi-omics solution - Stereo-CITE for high-plex spatial proteo-transcriptome co-detection. https://en.stomics.tech/
