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The RNA extraction: some procedures are more effective than others in removing gDNA (e.g., acidic phenol / chloroform extraction). It is therefore recommended to carefully evaluate the RNA extraction methods available, as they may also vary for the specific sample type used as input.
The library prep technology: the specific library prep can also influence the impact of gDNA levels on the sequencing results. 3’ mRNA-Seq library preps (like QuantSeq - Poole.g., QuantSeq) are less affected by the presence of low levels of gDNA contamination than random primed whole transcriptome library preps.
Nevertheless, high gDNA levels will also affect 3’ mRNA-Seq library preps and reduce the quality of the downstream data.The sample type: some samples can have a higher DNA / RNA content and therefore be prone to gDNA carry-over during RNA extraction.
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