I know that this question has been out for a while, but since I don't know whether you managed to address your experimental needs I'll suggest you have a look at the linked paper:
The authors have developed a RNA purification protocol compatible with intracellular antibody staining and fluorescence-activated cell sorting (FACS), showing that the protocol itself is amenable to isolate high quality RNA suitable for RNAseq, MicroArray andd qPCR.
I know that this question has been out for a while, but since I don't know whether you managed to address your experimental needs I'll suggest you have a look at the linked paper:
The authors have developed a RNA purification protocol compatible with intracellular antibody staining and fluorescence-activated cell sorting (FACS), showing that the protocol itself is amenable to isolate high quality RNA suitable for RNAseq, MicroArray andd qPCR.