We have extracted the RNA from birds’ fat tissues to perform high throughput sequencing. We detected that the fat also contain blood and thus many transcripts of hemoglobin proteins. We would like to know:
-Does someone know, approximately, what is the ratio of hemoglobin proteins in the total transcriptome of birds?
-Is there any possible “cleaning” solution to get rid of the RNAm of hemoglobin proteins?
Hello,
Might i ask why you want to get rid of these sequences ? I ask this because you could just get rid of the sequences using bioinformatics. You could isolate RNA from the blood of the same birds, then just delete the profile you observed in the blood from your fat data. If you are specifically concerned about hemoglobbin, specifically of the RNAm of a certain protein you could use custom RNA or DNA sequence conjugated with magnetic beads to link specifically hemoglobin RNAm. This would be the same approach as for getting rid of ribosomal RNA. However, this could be costly and might not get rid of all sequences. Unless your sequencing offers very little sequencing depth, i would rather sequence it as it is and then use bioinformatics to get rid of contaminants. Anyways sequencing will only give you insight on which sequence are found in your samples and you will need to validate those which you could do on "cleaner" blood free sample you could gather later-on by perfusing the birds with PBS for example before sacrifice.
We did not obtain too much RNA from the fat. We are afraid of losing too much depth if a big fraction of our RNA belongs to hemoglobin. The fat samples came from biopsies (non-destructive sampling) so it is not possible to obtain completely “clean” samples.
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