single cell RNA seq on Fixed cells

Question

[shrish03]

Hello, I wanted to do single cell RNA seq on a very rare cytokine population. Which means I will have to do intracellular staining and then sort the cytokine producing cells. Inorder to detect cytokines, I will have to fix my cells and I read the fixing kills the cells and there is no RNA. is there a way to do single cell RNA seq on fixed cells ?? My single cell RNa seq system is by a company called Fluidgm (C1 system). Thanks !

[Michael]

You should ask this on seqanswers, as it is slightly off-topic for Biostars.

Answer 1

[Charles Plessy]

In addition to the question of the quality of the RNA-seq libraries, I recommend to verify that your fixed cells can be efficiently captured in the C1 flow cells.

Answer 2

[WouterDeCoster]

Sounds like a rather tricky experiment to me, perhaps the following paper is of interest for you: http://science.sciencemag.org/content/353/6294/78

Is there something else that characterizes your cells of interest? How rare is the population?