High throughput quantitative whole transcriptome analysis of E18.5 mouse distal lung mesenchyme and endothelium

We used microfluidic single cell RNA-seq on 42 individual mouse lung mesenchymal and 69 endothelial cells at E18.5 to measure the transcriptional state. We were able to classify these cells into distinct populations as well as map their signaling interactions with the distal lung epithelium. In this manner, single cell RNA-seq can be used to unbiasedly determine the signals the dictate construction and maintenance of the alveolus. Overall design: 42 single-cell mesenchymal and 69 endothelial transcriptomes from E18.5 mouse lung were analyzed in total and NTC and three 200-cell bulk control sample; All single cell and control samples contain 92 external RNA spike-ins; In a single E18.5 timepoint, 111 transcriptomes were isolated; In addition,three 200-cell bulk control sample was prepared for E18.5;All single cell samples were processed on the microfluidic platform, 200-cell-bulk control sample was processed in microliter volumes in PCR tubes.