Protocol to combine brain sections from multiple mice into a single block for spatial transcriptomic analyses

Yoshitaka J Sei; Myriam M Chaumeil; Ken Nakamura

doi:10.1016/j.xpro.2023.102617

Protocol to combine brain sections from multiple mice into a single block for spatial transcriptomic analyses

STAR Protoc. 2023 Dec 15;4(4):102617. doi: 10.1016/j.xpro.2023.102617. Epub 2023 Sep 23.

Authors

Yoshitaka J Sei¹, Myriam M Chaumeil², Ken Nakamura³

Affiliations

¹ Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA.
² Department of Physical Therapy and Rehabilitation Science, San Francisco, CA 94158, USA; Department of Radiology and Biomedical Imaging, San Francisco, CA 94158, USA; UCSF/UCB Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA 94158, USA; Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA.
³ Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Program in Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA; Graduate Program in Neuroscience, University of California San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: ken.nakamura@gladstone.ucsf.edu.

Abstract

Spatial transcriptomics couples visual spatial markers with gene expression levels, but slide space and cost limit the number of samples that can be processed. Here, we present a protocol for mounting brains from multiple mice onto a single capture area of a spatial transcriptomics slide. We describe steps for conjoining frozen hippocampal sections from different brains into a single cryostat block, reducing the quantity of reagents required. This protocol is applicable to a range of existing spatial genomics platforms. For complete details on the use and execution of this protocol, please refer to Li et al. (2023).¹.

Keywords: Biotechnology and Bioengineering; Genomics; Neuroscience.

MeSH terms

Animals
Brain
Gene Expression Profiling*
Genomics
Hippocampus
Mice
Transcriptome* / genetics

Abstract

MeSH terms

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