You might want to give the PicoPure kit a go. It is available from Thermo Fisher here in the US. They claim that it can be used to isolate RNA from as few as 10 cells. I have used it to get RNA from 40,000- 50,000 cells.

Hi,

We use miRNeasy Micro Kit from Qiagen (cat. no. 217084) for RNA-Seq (usually >1000 FACS-sorted cells). Anyway, it should also work with lower numbers of cells. The important step is to use Isopropanol instead of Ethanol for preparing solutions (they describe it in the kit supplementary) as well as to perform DNAse treatment. The only way to check the quality of such low-concentrated RNA is to run it on the RNA-Pico BioAnalyzer (NanoDrop will show random number due to Qiazol-derived phenol traces in the sample, and Qubit RNA will show "nn" due to too low concentration). Anyway, even if you do not see much on the BioAnalyzer (which could definitely happen for hundreds of cells with small cytosol), but the samples are too precious, or if you see that your RNA is degraded, you may consider to use the Clontech Pico (SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian), which allow 250 pg - 10 ng input, which is actually the closest kit I know to the single-cell RNA-seq resolution (1 cell has roughly 10 pg of RNA). It can work with degraded RNA because it is not polyA-based, but whole transcriptome, which use random priming for cDNA synthesis, that’s why it is independent from the RNA integrity. Also it does the initial cDNA synthesis and preampfification before depletion of ribosomal RNA, which also allows to work with lower input amounts in comparison to kits which do the ribosomal depletion at the very beginning.

Best,

Michail

Qiagen RNeasy Micro or the PicoPure kit are your best bet.