Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas.
The method described here aims at the construction of a single-cell resolution gene expression atlas for an animal or tissue, combining in situ hybridization (ISH) and single-cell mRNA-sequencing (scRNAseq).A high resolution and medium-coverage gene expression atlas of an animal or tissue of interest can be obtained by performing a series of ISH experiments, followed by a process of image registration and gene expression averaging. Using the overlapping fraction of the genes, concomitantly obtained scRNAseq data can be fitted into the spatial context of the gene expression atlas, complementing the coverage by genes.
Gene Expression Regulation
Vergara, Hernando Martínez
1. Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics.
2. Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes.
3. Significance of single-cell and spatial transcriptomes in cell biology and toxicology.
4. Single-cell-level spatial gene expression in the embryonic neural differentiation niche.
5. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution.
1. ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes
2. Seq-Scope: Submicrometer-resolution spatial barcoding technology that enables microscopic examination of tissue transcriptome at single cell and subcellular levels
3. Single-cell sequencing of stage 4 chicken embryos
4. E14.5 wild type mouse embryo microarray results
5. Spatial reconstruction of single-cell gene expression