Gene expression atlas of a developing tissue by single cell expression correlation analysis

The Drosophila wing disc has been a fundamental model system for the discovery of key signaling pathways and for our understanding of developmental processes. However, a complete map of gene expression in this tissue is lacking. To obtain a complete gene expression atlas in the wing disc, we employed single-cell sequencing (scRNA-seq) and developed a new method for analyzing scRNA-seq data based on gene expression correlations rather than cell mappings. This enables us to discover 824 genes with spatially restricted expression patterns, and to compute expression maps for all genes in the wing disc. This approach identifies both known and new clusters of genes with similar expression patterns and functional relevance. As proof of concept, we characterize the previously unstudied gene CG5151 and show it regulates Wnt signaling. This novel method will enable the leveraging of scRNA-seq data for generating expression atlases of undifferentiated tissues during development. Overall design: Single cell transcriptome experiments from female wandering 3rd instar wing discs were generated: two samples using Drop-seq and one sample using the 10x genomics platform. Bulk polyA-RNA-seq experiment from the same tissue was conducted for comparison.

果蝇翅盘（Drosophila wing disc）是发现关键信号通路、解析发育进程机制的经典模式系统。然而目前仍缺乏该组织完整的基因表达图谱。为构建翅盘完整的基因表达图谱，我们采用了单细胞RNA测序（single-cell RNA sequencing，scRNA-seq）技术，并开发了一种基于基因表达相关性而非细胞映射的scRNA-seq数据分析新方法。该方法使我们得以鉴定出824个具有空间限制性表达模式的基因，并计算出翅盘内所有基因的表达图谱。此方法不仅能识别出具有相似表达模式与功能相关性的已知基因簇，还能发现新的基因簇。作为概念验证，我们对此前未被研究的基因CG5151进行了功能表征，并证实其可调控Wnt信号通路（Wnt signaling）。这种新颖的方法将助力利用scRNA-seq数据构建发育过程中未分化组织的基因表达图谱。

整体实验设计：针对雌性游走期三龄幼虫的翅盘开展单细胞转录组实验：采用Drop-seq技术构建2个样本，采用10x Genomics平台构建1个样本。同时针对同一组织开展了批量polyA-RNA测序实验以作对照。