My advice would be: Don't. Well, yes on the transcriptome sequencing, pretty much every commercial NGS provider will do it although be aware of sources of contamination, especially if you outsource your library prep. And if your culture isn't pure you'll have a hard time someone else contaminated your library.

But most commercial NGS services do pretty standard shotgun bioinformatics analyses in a very standard way. This may not be appropriare depending on what organism you are working with. What supergroup is your particular protist in? You would probably be better off finding someone to collaborate with on the transcriptome in terms of annotation and functional assignment if you aren't confident doing it yourself. You'll get much better results, and deposit much better information to the community as scientific data this way.

There are several providers on Genohub who can make RNA-Seq libraries, sequence and annotate your protozoan. Just click to connect with one of them: https://genohub.com/shop-by-next-gen-sequencing-project/#query=6f5e88af1dbc3df1f309ef91d63581e2

--Genohub