High throughput quantitative whole transcriptome analysis of adult mouse distal lung mesenchyme

We used microfluidic single cell RNA-seq on 47 individual mouse lung mesenchymal cells at adulthood 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 and endothelium. In this manner, single cell RNA-seq can be used to unbiasedly determine the signals the dictate construction and maintenance of the alveolus. 47 single-cell transcriptomes from adult mouse lung mesenchyme were analyzed in total and one 200-cell bulk control sample; All single cell and control samples contain 92 external RNA spike-ins; In a single adult timepoint, 47 transcriptomes were isolated; In addition, a 200-cell bulk control sample was prepared for this adult timepoint;All single cell samples were processed on the microfluidic platform, 200-cell-bulk control sample was processed in microliter volumes in PCR tubes.