In the present study, we used massive parallel DNA sequencing coupled with an unbiased analytic approach to identify molecular mRNA signatures in single cells isolated from the entire embryonic mouse lung at the saccular phase (E16.5) of morphogenesis. Through integrative bioinformatics and systems biology analysis of single-cell RNA-seq data, we identified major cell types in the E16.5 fetal mouse lung. A diversity of epithelial, endothelial, smooth muscle, pericyte, bone marrow derived, and several fibroblastic cell subtypes were classified by their RNA expression similarity within cell type groups (Figure 1). Unique cell-specific gene signatures, key regulators, cell surface markers associated with each cell type were identified. The data provide a rich information base facilitating the understanding of lung maturation at high resolution and identifying the genetic framework that regulates cell fates during lung maturation (Supported by U01 HL122642 and U01HL110964).

Single Cell Lung Map provides gene centric and cell type centric web-tools to query cell type specific gene expression. For any input gene, the tool will produce heatmap, bar graphs and expression statistics across all cell types. Top 20 most correlated genes and dynamic expression patterns during lung maturation will also be displayed. For any selected cell type, the tool will retrieve cell type specific gene signatures, surface markers and transcription factors associated with the cell type. The current tool is built using the lung single cell RNA-seq data from E16.5. We will extend the usage to other developmental data points and different species (mouse, monkey, human) as the project moves forward.