Hi all,

I was planning to send RNA samples collected from Arabidopsis root tissue for standard RNA sequencing. All of these samples were processed in the same way except in the DNase removal step. I used the RapidOut DNA Removal Kit (Thermo Scientific) according to the manufacturer’s instructions. To remove the enzyme, I used the DNase Removal Reagent (DRR) that came with the kit on 16 of the 24 samples (before realizing that I would not have enough for all the samples). For the remaining 8 samples, I used EDTA at a concentration of ~4.5 mM and heat-inactivated the DNase at 75C for 5 min. For all samples, my RNA concentrations were similar (170-230 ng/ul) and my 260/280 values were greater than 2.0 as measured with a Nanodrop. My 260/230 values were between 1.7-2.0 for the 16 samples processed with the DRR and slightly lower (~1.4 - 1.6) for the samples processed with EDTA + heat-inactivation (which was not surprising, as EDTA absorbs at 230 nm). My question is, will this affect the final outcome of the RNA-Seq in terms of comparing gene expression between samples? Any advice on what to do in this case?

thanks for your scientific insight!