Hello, I have extracted my RNA from a virus and I want to sequence using NGS, the RNA sample has Mycoplasma arginini contamination. I would like to eliminate the bacterial contamination before preparing the Library for sequencing. How do I do this?
Faustino Delgado Camacho
Detection studies, especially with a diagnostic focus, should incorporate stringent SOPs across the entire experimental pipeline from sample collection to sequencing. Highly purified metabolic enzymes and other reagents used in sequence library preparation should be used whenever possible. Standards for the curation of microbial sequences submitted to Genbank and other large-scale databases should be established in order to assess completeness and quality of the assembled genomes. Contamination controls such as mock sequence library preparations should be used to help guide the development of appropriate and effective SOPs for metagenomic and metatranscriptomic studies.
I agree with Mathew, for some cases, contamination can potentially be dealt with bioinformatically. One approach would be to utilize a repository of common contaminating organisms to sort them out.
Strong et al proposed the following recommendations:
Source: PMC4239086
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Laurence Stuart Dawkins-Hall
I would fix the problem at source by making a new RNA prep free of Mycoplasm; if you can. If you can’t you have been offered some excellent advice above
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