空间转录组学：构建单细胞分辨率的全转录组表达图谱。

Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas.

作者信息

Achim Kaia, Vergara Hernando Martínez, Pettit Jean-Baptiste

机构信息

Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire, CB10 1SD, UK.

出版信息

Methods Mol Biol. 2018;1649:111-125. doi: 10.1007/978-1-4939-7213-5_7.

DOI:10.1007/978-1-4939-7213-5_7

PMID:29130193

Abstract

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.

摘要

本文所述方法旨在构建动物或组织的单细胞分辨率基因表达图谱，结合原位杂交（ISH）和单细胞mRNA测序（scRNAseq）。通过进行一系列ISH实验，随后进行图像配准和基因表达平均化过程，可以获得感兴趣的动物或组织的高分辨率和中等覆盖度基因表达图谱。利用基因的重叠部分，可将同时获得的scRNAseq数据拟合到基因表达图谱的空间背景中，补充基因的覆盖范围。