Mitochondrial genome in Tru RNAseq

[biochembug]

Hi folks,

What percent of a RNAseq library can be mitochondrial genome? I understand that it should not be there after DNase I treatment. Despite, I have done 2 rounds of oligo dT, I am seeing some hits to mitochondrial genome. Is this common?

Biochembug

[protist]

Are you sure they are not mitochondrial transcripts. It depends on the organism that you are working with but various euks polyadenylate both nuclear and mitochondrially derived transcripts - with oligo dT selection those polyA-mito RNAs would be carried through the library prep.

[biochembug]

Hi there

I am talking about a pGEM-T clone obtained from a Truseq library. When I blast the sequence with Refseq RNA db using BLASTN, it gives no significant hit. However, after BLASTX it had some similarities to cytochrome oxidase. Also when aligned with genome, it gives best and 100% coverage to mitochondrial genome.

Biochembug