This is something that I have been working with recently and the answer is that no method does this. As Kenneth says, forget the bioanalyzer, I tried and it doesn't work. And this is the most sensitive method, so you have to attack the problem from another angle. If you are simply interested in the amount of total RNA in a single cell then I'd simply pick 100 cells, run the bioanalyzer and divide the answer by 100. However, considering your question you don't seem to have this luxury! What then? Well I would run a first strand cDNA synthesis and then run a PCR, you may even consider qPCR. These will give you a slight indication of quality and quantity but the reality is that you will be almost working blind! I guess this is something that will improve with the dawn of pacbio.

Pico chip on bio-analyzer will solve your problem.

The Bioanalyzer products are very useful, but not even the Pico chip is this sensitive. A single cell might contain about 10 pg of RNA. Assuming 100% recovery of RNA and concentration of the volume to 1 ul (the input requirement for the Pico chip), 10 pg/ul is still well below the 50 pg/ul lower limit of the Pico chip's range. Additionally, no RNA would remain for other measurements.

Why not simply normalize to cell count? Similar to biofluids RNA experiments, where recovered RNA is also quite low and input is normalized to volume.

Use the theory of sampling. Be accurated in counting many pool of cells. Extract the RNA for them. Quantify the RNA and estimate with a significant confident (probabilities below the error effect) the total RNA per cell ± desviation. Practical, razonable and methodological way.

This is something that I have been working with recently and the answer is that no method does this. As Kenneth says, forget the bioanalyzer, I tried and it doesn't work. And this is the most sensitive method, so you have to attack the problem from another angle. If you are simply interested in the amount of total RNA in a single cell then I'd simply pick 100 cells, run the bioanalyzer and divide the answer by 100. However, considering your question you don't seem to have this luxury! What then? Well I would run a first strand cDNA synthesis and then run a PCR, you may even consider qPCR. These will give you a slight indication of quality and quantity but the reality is that you will be almost working blind! I guess this is something that will improve with the dawn of pacbio.

Thanks for your replies.

We do not have a working bioanalyzer as yet.

If it is a pool of single cells (like oocytes), the method of normalization to cell count could work.Quantifying total RNA from 100 oocytes and then assuming all the oocytes have the same concentration of total RNA, we can probably arrive at some value for a single oocyte.

But when it comes to cleaved cells, like morula or blastocyst, the number of cells in a fixed number of blastocyst/morula is not defined.So that is where we need to fix the concentration of RNA to proceed for cDNA synthesis & eventually qPCR.

Not for total RNA, but if you are interested in a particular RNA, you can probe it using this kit... http://www.acdbio.com/products/rnascope-assays/rnascope-fl/. For total I would use qPCR.

Moloya, to quantify cleave cells also it is possible use the quantified cells vs RNA, just made a model (you can start with a lineal one) just quantify the RNA from a known number of cell and a known stage of develop. The model may give one approach to infer the RNA with statistical parameters on the base a good number of replicates. Other way in the same approach is also incorporate markers that can be used as quantitative reporters. One problem may be that some cells are inactive in transcription just until late cell cycles. So just do the best.