Coverage dept needed for Exosomes

[diego diaz]

Hi all,

In my lab, we want to characterize (only characterize, not differential expression) RNA elements inside of exosomes, by using sequencing. My bosses want to make a pool of several samples.

I think is different than conventional RNA-seq because we aren't going to use all the transcriptome, only the exosomes.

Do you have any idea of the minimum depth needed for this kind of analysis?

Thanks in advance!

[diego diaz]

Other question. My bosses said to me that in literature has been reported that the exosomes can contain some mRNA molecules. To exosome profiling is more suitable using total RNA-seq (smallRNA + mRNA) or only smallRNA-seq?

thanks in advance!

[GenoMax]

Not directly able to answer you question (in this case how do you define significant "depth"? A single read, could (in theory), represent a real rare RNA).

There are many "exosome" labeled datasets in SRA: http://www.ncbi.nlm.nih.gov/sra/?term=exosome You may want to look through those and associated publications (if any).

[diego diaz]

Thanks GenoMax !

[diego diaz]

About the second question, what do you think is the best approximation to perform the analysis? smallRNA-seq or total RNA-seq?