I first posted this over on SeqAnswers, but figured cross-posting may be ok.
My lab is studying a cell population in Drosophila that is difficult to isolate, but genetically tractable. We created some flies in which we have genetically ablated the cells of interest using the GAL4/UAS system to induce apoptosis. We have collected control and experimental samples in triplicate and performed a paired-end RNA-Seq experiment using the Illumina HiSeq platform.
We are now analyzing the data. My question is whether anyone has seen examples of this kind of approach before.
Since the cells in question make up only a small proportion of the isolated tissue, we expect that most of the down-regulated genes will be fairly specific to this particular cell type. Up-regulated genes will likely be related to the induction of apoptosis itself and the process of cleaning up the mess.
Has anyone tried this sort of approach on cell types whose expression profiles are otherwise difficult to assess.
I have tried searching Google Scholar for as many search terms as I can think of to identify papers doing something like this, but I have so far come up empty. I guess this either means I am a pioneer or an idiot.
Any comments or references would be helpful. Also warnings on things we will need to be aware of during data analysis.