Feb 17, 2017

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

Nature Protocols
Jun ChenNaihe Jing

Abstract

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 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 ...Continue Reading

  • References42
  • Citations44

Mentioned in this Paper

Single-Cell Analysis
Embryo
In Vivo
Sequence Determinations, RNA
Entire Embryo
Spatial Distribution
Brain
Nucleic Acid Sequencing
Lymphocytic Choriomeningitis
Gene Expression

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