Sci-Space E14 Mouse Embryo Data
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Summary
Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections.
Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections.
Overall design
Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derrived.
Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derrived.
Technology
sci-Space
sci-Space
Platform
GPL21626
GPL21626
Species
Mus musculus
Tissues
Embryo
Embryo
Submission date: 2021-02-12Update date: 2021-07-01
Accessions
GEO Series Accessions:
GSE166692