1] European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK. [2] Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
Nat Biotechnol. 2015 May;33(5):503-9. doi: 10.1038/nbt.3209. Epub 2015 Apr 13.
Understanding cell type identity in a multicellular organism requires the integration of gene expression profiles from individual cells with their spatial location in a particular tissue. Current technologies allow whole-transcriptome sequencing of spatially identified cells but lack the throughput needed to characterize complex tissues. Here we present a high-throughput method to identify the spatial origin of cells assayed by single-cell RNA-sequencing within a tissue of interest. Our approach is based on comparing complete, specificity-weighted mRNA profiles of a cell with positional gene expression profiles derived from a gene expression atlas. We show that this method allocates cells to precise locations in the brain of the marine annelid Platynereis dumerilii with a success rate of 81%. Our method is applicable to any system that has a reference gene expression database of sufficiently high resolution.
理解多细胞生物中的细胞类型身份需要将单个细胞的基因表达谱与其在特定组织中的空间位置进行整合。目前的技术允许对空间上确定的细胞进行全转录组测序，但缺乏对复杂组织进行特征描述的通量。在这里，我们提出了一种高通量的方法，可以识别在感兴趣的组织中通过单细胞 RNA 测序进行分析的细胞的空间来源。我们的方法基于将细胞的完整、特异性加权 mRNA 谱与来自基因表达图谱的位置基因表达谱进行比较。我们表明，这种方法可以以 81%的成功率将细胞分配到海洋环节动物 Platynereis dumerilii 大脑中的精确位置。我们的方法适用于任何具有足够高分辨率参考基因表达数据库的系统。
