I have done both RNA extractions using Trizol or Kit in mouse and rat tissues. From my experience Trizol is a very good method to do so but its efficiency and purity will depend on the ability of the user to correctly do the procedure. When talking about extraction kits, they are much more user friendly and are not as much dependent on the user but from my experience they also have the drawback of lower final RNA concentrations.

In summary it depends if you have the time to perfect your Trizol extractions or if you just want a fast and user friendly method but with a lesser yield.

I agree with André Furtado it depends on the user. Trizol works well as long as you don't end up with trizol contamination in your final samples. The kits also tend to be significantly more costly. So if cost is also a concern then I would go with trizol.

Thanks for chiming in André and Josh! I think André seems to have hit a lot of nails on the head. After gathering opinions from all over, I think the biggest key to people's preferences is time: RNeasy Plus mini kits take

Second follow-up: just re-found this question and can add new perspective after prepping the 150 sample RNAseq experiment from the OP:

Again, kits = faster than TRIzol centrifuging. But some kits (like the Zymogen Direct-zol kit) allow you to take samples in TRIzol and directly clean them on a column, and even do DNAse digest on the column as part of the extraction. This is the kit and approach I ended up using. It was fast (DNAse digest as part of column was great), and worked like a charm. The kits in general lose a lot more RNA than standard TRIzol extraction though.

e.g. https://www.zymoresearch.com/pages/direct-zol-rna-purification-kits

Recommendation:

1. Using a direct-zol kit to supplement TRIzol extractions lets you protect RNA and work quickly/comfortably if processing many samples. The workflow is also simplified compared to spin, pipette, spin, rinse, spin, rinse, elute, DNAse, etc... by allowing very short spins, and doing DNAse mid-prep.

2. If you expect low yield of RNA, I would not recommend kits. You could alternately try micro prep RNA kits, though I haven't. In general, there's no secret voodoo of prepping RNA for an RNAseq experiment. The only difference from most lab's procedures is just that you'll want to quantify RNA degradation using something like a Qubit bioanalyzer. The basic 260/280 and 260/230 ratios of a Nanodrop do a good job of telling you your RNA is at least clean. And if you've ever run your RNA on an agarose gel to check its degradation, you've already done the basic quality control that RNAseq demands in a low-budget form.