DNA Contamination Interferes with RNA Quantification and Depletion (RNA Depletion for RNA-seq)

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RNA depletion shows poor efficiency with high residual target reads. RNA quantification may be inaccurate and inconsistent with expected values. Common causes: 1) Contaminating genomic DNA causes inaccurate RNA quantification leading to improper probe:target ratios 2) DNA contamination physically impedes proper hybridization between probes and target RNA 3) Total RNA sample contains genomic DNA that was not removed during extraction Solutions: 1) Treat total RNA sample with DNase I (not provided in kit) to remove all traces of DNA contamination 2) Completely remove DNase I enzyme after treatment - residual activity will degrade single-stranded DNA probes 3) Verify RNA purity and absence of DNA contamination before proceeding with depletion protocol 4) Re-quantify RNA after DNase I treatment and removal to ensure accurate input amounts