Fluidigm C1 + Illumina HiSeq quantitative whole transcriptome analysis of unsorted population of E16.5 lung cells

We used microfluidic single cell RNA-seq on mixed e16.5 mouse lung cells in order to determine the potential cell types present based on differential transcriptional profiles of the entire population using minimal cell selection bias. Overall design: whole lung mouse e16.5 cells were pooled and loaded onto the Fluidigm C1 device. microwells that contained intact single cells were recorded, the labchip was processed for the generation of cDNA from each cell, and cDNA generated from each accepted well was used to generate amplified and barcoded DNA library that was loaded into an Iluumina HiSeq machine for HTS analysis.