Hi, I am preparing a new project on lncRNAs in human cancer cell lines. I scanned through many high-impacted journals to find the best RNA isolation kit that would also isolate small RNAs and that would be compatible with RNA-Seq. I noticed that pretty much everyone is using Trizol reagent for RNA extraction, followed by column-based purification, with three kits being the most popular: RNAEasy kit, miRVana kit or Trizol Plus kit (Trizol together with purification columns). Which column-based purification system is the best one, in terms of RNA purity and stability and good quality for subsequent lncRNA RNA-Seq, with possibility to run also small RNA-Seq for miRNAs in the future?
I've had great success using the Qiagen miRNEasy kits to purify RNA for RNAseq.
We've used this kit for downstream analysis of all types of RNA (e.g. miRNA, mRNA, lncRNA, circRNA) from a variety of samples including both tissue and cell culture.
I'm just starting to get involved in this area, so am interested in the answers to your question. Zymo Research market RNA preparation kits that allow fractionation of RNA into small (< 200 nt) and large RNA species. An interesting paper on the subject is Ford et al. (2019). 'Optimisation of laboratory methods for whole transcriptomic RNA analyses in human left ventricular biopsies and blood samples of clinical relevance.' PLoS ONE 14(3): e0213685 (https://doi.org/10.1371/journal.pone.0213685). They mention that "...TRIzol-based RNA extraction methods selectively lose miRNAs with low GC-content, when isolating RNA from low cell numbers,...". The paper in question eventually had to be retracted because of this error. Something to bear in mind...! Hope this helps.
Qiagen miRNEasy kits and Zymo based kits I have used previously with cell lines and both work fine for this kind of work.
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