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Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq
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Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq
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Journal Article
Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq
2017
Overview
Geo-seq combines laser capture microdissection and single-cell RNA-seq technology to enable transcriptome analysis of small quantities of cells from defined geographical locations.
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact
in vivo
or
in situ
position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use geographical position sequencing (Geo-seq), a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously. The Geo-seq protocol allows the profiling of transcriptome information from only a small number cells and retains their native spatial information. This protocol has wide potential applications to address biological and pathological questions of cellular properties such as prospective cell fates, biological function and the gene regulatory network. Geo-seq has been applied to investigate the spatial transcriptome of mouse early embryo, mouse brain, and pathological liver and sperm tissues. The entire protocol from tissue collection and microdissection to sequencing requires ∼5 d, Data analysis takes another 1 or 2 weeks, depending on the amount of data and the speed of the processor.
Publisher
Nature Publishing Group UK,Nature Publishing Group
