I need to calculate how much to sample of a microalgae culture to have around 100 ug of RNA. Any idea of how much cells/biomass is normally sampled for transcriptomics?
RNA should be related to the growth rate; it is also certainly very species specific (see, for instance, Giordano et al, 2015 Plant Cell and Environment. DOI: 10.1111/pce.12551). In that paper you can also get an idea of the amount of RNA in cells of a few species.
Some other estimate you can find in Norici et al. 2011 Plant Cell and Environment 34: 1666-1677 and in some of the papers cited there.
The other problem is yield. In my experience, the amount per cell you get from diatom, again for instance, is often much below what you would expect; i think it is a matter of yield more than actual amount contained in the cell.
I hope this helps, although is not the straight number i believe you were hoping for. Cheers, Mario
Thanks a lot for your answer. I know it is not an easy question and I was not really expecting to be a single number. Biology is never so easy! :) but to have an idea of what a range I should expect on average it is enough for me to start working. I will take a look at the papers you have recommend me. Thanks a lot for that. I am sure I will find them very useful!
As previously mentioned its not an easy question keep a few things in mind while extracting rna...phase of growth, cell volume, usually cell vol is directly proportional to DNA content but its not a rule. Also depends on your growth conditions..stressed conditions might be giving you a biased result. Transcriptomics can be done on 4-5 ug of RNA depending on your question which can take upto a million cells...100 ug might take a few litres of cultures. :) Good luck
Thanks for the answers, Gergley and Arjun. I will take in mind your comments and advices when developing my transcriptomics approach. Best wishes, Maria