Developing mouse whole-brain transcriptomic cell type atlas - MERSCOPE v1

Abstract

Spatial transcriptomics atlas of the entire brain of a developing mouse (P4). We profiled 500 genes which were selected to maximize our ability to relate each cell to one of the 5200 cell types defined in our RNAseq-based taxonomy. We image 14 µm section which were acquired at an interval of 100 µm. Individual cell were identified using cell segmentation algorithms to a total of ~9.2 million cells. The MERFISH datasets not only provide the possibility for accurate spatial annotation of major cell types at subclass level, but also reveal very fine resolution spatial distinctions or gradients for cell types within each subclass.

Contributors

• Kunst, Michael ORCID Allen Institute for Brain Science Researcher
• Mathieu, Remi ORCID Allen Institute for Brain Science Researcher
• Ching, Lindsey ORCID Allen Institute for Brain Science Researcher
• Quon, Jacob ORCID Allen Institute for Brain Science Researcher
• McMillen, Delissa ORCID Allen Institute for Brain Science Researcher
• Nagra, Josh ORCID Allen Institute for Brain Science Researcher
• Olsen, Paul ORCID Allen Institute for Brain Science Researcher
• Campos, Jazmin ORCID Allen Institute for Brain Science Researcher
• Martin, Naomi ORCID Allen Institute for Brain Science Researcher
• Ariza, Jeanelle ORCID Allen Institute for Brain Science Researcher
• Ruiz, Augustin ORCID Allen Institute for Brain Science Researcher
• Valera Cuevas, Nasmil ORCID Allen Institute for Brain Science Researcher
• Waters, Jack ORCID Allen Institute for Brain Science Researcher
• Zeng, Hongkui ORCID Allen Institute for Brain Science ProjectLeader
• Allen Institute for Brain Science ResearchGroup
• Arlotta, Paola ORCID Harvard Stem Cell Institute ProjectLeader

Funding

• National Institutes of Health 5-U01-MH130962-02 Comprehensive single-cell atlas of the developing mouse brain

Data