We are carrying out RNAseq on some human tissues and have been facing rRNA contamination issues.
We first carried out library prep with the Ribozero and while this depleted most of the cytoplasmic rRNA we noticed that there was still mitochondrial contamination. We therefore switched to the Ribozero-gold and the were happy that the mitochondrial rRNA were also eliminated.
On further QCing on the latest samples we noticed that there were a lot of reads that were now mapping to GL000220.1, an unplaced contig in GRCh37 which has a number of rRNA genes annotated in it. Since this is unplaced we did not check this initially.
My questions are
1. Is anyone else aware of this issue?
2. Are the kits from epicentre expected to remove RNA related to this contig as well?
3. Are there other ways to eliminate them during library prep that does not involve doing polyA?
Any help/suggestions/links would be great. Happy to provide further details if required.
Thanks
We first carried out library prep with the Ribozero and while this depleted most of the cytoplasmic rRNA we noticed that there was still mitochondrial contamination. We therefore switched to the Ribozero-gold and the were happy that the mitochondrial rRNA were also eliminated.
On further QCing on the latest samples we noticed that there were a lot of reads that were now mapping to GL000220.1, an unplaced contig in GRCh37 which has a number of rRNA genes annotated in it. Since this is unplaced we did not check this initially.
My questions are
1. Is anyone else aware of this issue?
2. Are the kits from epicentre expected to remove RNA related to this contig as well?
3. Are there other ways to eliminate them during library prep that does not involve doing polyA?
Any help/suggestions/links would be great. Happy to provide further details if required.
Thanks
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