We characterized gene expression profiles in founder cells isolated from Drosophila embryos.

Staged, rp298>eGFP embryos were grown at 25C and collected at 7-10hr after egg lay. Approximately 200mg of embryos were collected and dissociated with elastase. The cell suspension was incubated with Hoechst (1μl/ml, Invitrogen), and sorted on a FACSAria cell sorter. Minimum fluorescent intensity gates were established for GFP and Hoechst by standard methods. GFP+, Hoechst+ cells were collected for the experimental population and GFP-, Hoechst+ cells were collected for the control population. Immediately after sorting, RNA was extracted with the RNeasy Mini kit cDNA libraries were generated with the TruSeq stranded mRNA sample library kit. High throughput RNA sequencing was performed using 50bp single-reads on the Illumina HiSeq 2000 system. Three biological replicates were sequenced for each cell population.