We want to sequence RNA from passerine bird blood to look at host expression. We will need to remove the ribosomal RNA and also the globin RNAs during the library preparation. There is no reference genome available for this species; the closest species is zebra finch. Normally the sequencing service would use the Illumina Globin Zero depletion with Truseq directional library preparation, however I understand this is unlikely to be successful for my RNA as the optimisation is for Human/mouse/rat.
Does anyone know of another option that may be more successful when using RNA from birds?
Hi Daisy,
There is not likely to be an easy (kit based) answer for what you want to do.
I would sequence the globin message (based either on low depth RNA seq on blood or amplicons generated with primers based on closest available genetic relative).
Generate a bait library based on your sequence and perform the depletion yourself.
Since it seems your rely on the sequencing service for your library prep this may be difficult for your lab. Depending on your relationship with the sequencing facility you may be able to work with them to achieve this.
Maybe someone else will have an easier way, but I am not optimistic.
I don't know if there is a way to actually physically remove just the rRNA and globin RNAs during your sample prep.
But, you should be able to parse them out bioinformatically once you have your data.
I Daisy, did you get your question answered? I just saw your question. I managed the most recent assembly of the zebra finch genome.
https://www.researchgate.net/post/Reduce_hemoglobin_in_RNA_extracted_from_bird_blood_for_Illumina_sequencing
The zebra finch sequence will work just fine. If you have any questions about your project, email me at [email protected]
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