If you are using a Trizol protocol for the RNA extractions we would highly recommend cleaning the samples afterwards with a spin column kit (e.g. On Bioanalyzer RNA-chips, DNA contamination will be visible in the size range 4 kb to 10 kb. On an agarose gel, DNA contamination will be visible as a smear or band of fragments considerably larger than the RNA (>10 kb). The RNA isolation protocol should always include a DNase digestion step in problematic cases use RNA-clean & concentrator kits with DNase.
Please find our suggestions for affordable solutions for Illumina sequencing below. Multiple protocols are available to remove DNA or RNA contaminants. In these cases the nucleic acid samples contribute very little to the signal and the slightest contamination dominates the readings. The spectrophotometer ratios themselves become easily misleading at very low DNA or RNA concentrations (10 ng/ul or less).One can vent the open sample tube (for example for 20 minutes) on the lab bench and measure again afterwards to see if the contamination has disappeared. Any organic substance, including ethanol, will skew the 260/230 nm ratios. In case the absorption ratios are skewed, it is often worth checking if any alcohol was carried over from the spin column or bead washes.However, it is certainly helpful to also record the entire UV absorption spectrum as it provides additional information. Please see the sample requirements page for the recommended values for your protocol. The 260/230 nm and 260/280 nm absorption ratio measurements are most frequently used to assess purity.Skewed absorption ratios indicate that there is chemical contamination, but not precisely which contaminant and if it will be deleterious or not, Please see this guide from the University of Arizona on the interpretation of Nanodrop data.Please test for chemical contamination by spectrophotometry (e.g., Nanodrop), concentrations should be measured by fluorometry instead (Qubit, Quantus, plate reader, …) : For genomic DNA samples to be sequenced on Illumina sequencers, we suggest spin columns since DNA treated this way will always dissolve well and completely. Bead based sample cleanups (e.g., Ampure XP, RNAClean XP) and spin column-based protocols ( e.g., Qiagen, Zymo, NorgenBiotek) tend to be the most efficient ways to remove chemical contaminants.
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