Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were unable to eliminate the genomic E. coli contamination. We designed a primer targeting a highly abundant E. coli gene present in our RNA-seq data and checked for contamination after each step and reagent. We discovered that the RNase inhibitor from A&A Biotechnology was the source of the contamination. Therefore, I highly recommend against using this product for RNA-seq experiments.
Yes, this was not a question. I'm unsure where to share this information. After spending four months identifying the source of contamination, I want to share my experience to help others avoid similar issues.
Had the same issue with some of their PCR kits - contaminated with T7Express E. coli DNA.
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