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For single-infected cells, an RNA lysate clean-up was performed with RNAClean XP beads (Agencourt) prior to reverse transcription (RT).
Rapid sand filtration (RSF) is used today as an effective pretreatment procedure to enhance water quality prior to reverse osmosis (RO) membranes in desalination plants.
Prior to reverse transcription, RNA was quantified using a Qubit fluorometer (Invitrogen).
Prior to reverse transcription, RNA samples were treated with rDNAse I (DNA-free kit, Applied Biosystems).
RNA samples were DNAse treated prior to reverse transcription using the TURBO DNAse kit (Ambion, Huntingdon, UK).
The absence of DNA from RNA samples was verified by PCR prior to reverse transcription, using rpoB-specific primers.
To deal with this, minimization of secondary structure by fragmenting the RNA prior to reverse transcription (RT) was recommended.
Moreover, all mRNA samples were treated with DNase prior to reverse transcription and tested for genomic contamination with a primer set for the housekeeping gene GAPDH.
Prior to reverse transcription, a DNase digestion step was performed with DNaseI (Roche Diagnostic) and efficient digestion was controlled by gel electrophoresis.
As before, the region surrounding the apparent splice site was amplified from genomic DNA, cloned, transcribed, purified (Fig. 3C), and diluted with HeLa RNA prior to reverse transcription.
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Hydrolysates were decolorized with charcoal, filtered through a 0.65 μm filter (Millipore) (Sigma Aldrich) and then derivatized with 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (Acros Organics, ThermoFisher Scientific) prior to reverse-phase HPLC (Agilent 1100 series, Agilent Technologies) for the isolation of hydroxyproline with an acetonitrile gradient using a LiChrosopher, 100 RP-18 column.
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