Best method for RNA extracton for Illumina sequencing

[Old guy]

I am working with samples that are mixed Prokaryotic and Eukaryotic Cells, looking at prokaryotic gene expression in food. I don't work with RNA often and would like suggestions on the best method for total RNA extraction (I have only used Trizol in the past with mixed results).
To enrich for the prokaryotic mRNA, after extraction I am planning on using Epicentre's Ribo-Zero™ Magnetic Gold Kit for removal of rRNA.
Any other suggestions for enrichment?
After all that, Illumina has suggested using the TruSeq® Stranded mRNA Sample Preparation.

[ZWB]

I do mixed population (host/pathogen) RNA-Seq often and we always use the Direct-Zol kit from Zymo to do our extractions. This kit combines the advantages of Trizol with the ease of a column and always give us high-quality, high purity RNA. I've found that removal of rRNA by itself doesn't do much to enrich for the bacterial transcripts. If you know what bacteria you are looking for, I've devised a method to capture those transcripts that highly effective. Check the link below for a recent publication (first link). If you don't know what bacteria are present, you can use the Microbe-enrich kit from Ambion and/or use a differential lysis/filtration method to enrich for the bacteria up front (second link). Finally, we use a variation of the Clontech stranded RNA-Seq kit that we developed in house to create the libraries (third link). Best of luck with your experiments.

Zach

http://www.ncbi.nlm.nih.gov/pubmed/24155975

http://www.ncbi.nlm.nih.gov/pubmed/24286981

http://www.ncbi.nlm.nih.gov/pubmed/23558773

[Old guy]

Thanks for the reply. I think I will try the Direct-Zol kit from Zymo along with either Microbenrich or MicrobExpress.

[jwfoley]

I've tried the Zymo kit and I'm extremely skeptical of its DNase (lyophilized? resuspended in pure water?? frozen and thawed?!?). If you're concerned at all about genomic DNA contamination, you may want to do a normal DNase treatment in solution and repurify. For whole-transcript RNA-seq this isn't usually an issue though, and the Zymo kit is cheap and fast otherwise (although the columns are poorly made).

[Wallysb01]

I’ve had good results with the miRVana kit.