A little more information would be useful is it a consistent problem or just a one time thing? First thing  I would try is just re-extract the RNA.

Thanks steve. Its a problem which we are noting when we reduce the cell number. We first pass the cells through a sucrose gradient and collect 10 fractions ( do not pool monosomes 1-4 and polysomes 5-10). Following which we subject it to a sucrose cleanup ( sds+ 5m nacl + etoh) overnight and then treat it with trizol. Have tried additional phenol clean up using a commercial microkit. The 260/280 readings are

It's a common problem that you don't get good phase separation under high sucrose conditions, and the RNA recovery across different sucrose concentrations (as found across polysome fractions) is variable as well.There's a good description of the associated problems and solutions (including protocols) in the Clancy et al. 2007 Methods paper PMID 17923232. The two main ideas described in there are: (1) add heterologous spike-in RNA to each fraction, which will allow you to correct for differential recovery and (2) first precipitate the RNA from the sucrose-containing fractions with ethanol and then use Trizol on the washed RNA pellets.

Thank you David. Appreciate your input. We are currently EtOH ppt the poly and monosome fractions O/N before adding Trizol. Will consider incorporating the heterologous spike-in RNA.