There are many methods of RNA extraction available, both manual and commercial. The choice of method needs to be guided by the nature of the initial material, biopsy, tissue culture sample, high or low cell number yield, etc. Commercially available kits perform well enough, have the advantage of not requiring phenol extraction (with the exception of Trizol®, Invitrogen Life Technologies) but are costly. They do provide an advantage when low RNA yield is expected. However, when samples coming from tissue culture, where experiments are repeatable, manual extractions are better justified.
An important point is to verify the absence of genomic DNA contamination. A DNase treatment step may be included to follow RNA extraction as gDNA contamination may interfere with the assay. Different methods and kits are available. None is particularly better, but a column-based technique may be easier for inexperienced users.
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