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Hi,
does anybody have experience with designing a set of probe for rRNA depletion? there are some databases and programs out there but they are mostly for bacteria while I would need a specific application for Homo sapiens. I went through a few patents (those describing the oligos in the Ribozero, Ribogone, GeneRead kits, etc etc) but there are 2 major problems:
- for some the probes are too long, sometimes even full-length --> performance will be poor
- for most of the others their number is simply too high! --> astronomical cost!
Since it´s not needed to achieve full coverage of every possible rRNA base in order to achieve a good depletion, I would need some database/program able to give me the minimum set of probes.
Any suggestion is appreciated, thanks a lot!
/Simone
does anybody have experience with designing a set of probe for rRNA depletion? there are some databases and programs out there but they are mostly for bacteria while I would need a specific application for Homo sapiens. I went through a few patents (those describing the oligos in the Ribozero, Ribogone, GeneRead kits, etc etc) but there are 2 major problems:
- for some the probes are too long, sometimes even full-length --> performance will be poor
- for most of the others their number is simply too high! --> astronomical cost!
Since it´s not needed to achieve full coverage of every possible rRNA base in order to achieve a good depletion, I would need some database/program able to give me the minimum set of probes.
Any suggestion is appreciated, thanks a lot!
/Simone