The RNA will be used for the metatranscriptome sequencing analysis. But I'm not sure which method is the best to eliminate the rRNA from the unknown community RNA.
Ribominus (from lifetechnologies) and ribozero (from epicenter, illumina) are both good. Ribominus is much cheaper but from our lab's own experience a sample should be treated twice with the kit to completely deplete ribosomal RNA. Taking this in consideration, the price of one sample using ribozero or ribominus becomes the same, this is why we prefer ribozero. They have kits for bacteria, yeast, plant and human/mouse/rat.
Perhaps the ribozero kit from epicentre would be suitable:
http://www.epibio.com/applications/rna-sequencing/rrna-removal/ribo-zero-rrna-removal-kits-(bacteria)
You must use rRNA depleted RNA as a starting material to prepare a good quality meta-trancriptome libraries using any commercial kit.
The ribozero kit is designed to deplete 18s and 28s rRNA from a variety of gram negative and positive bacteria. Human/Rat/Mouse and Globin kits are also available.
Ribominus (from lifetechnologies) and ribozero (from epicenter, illumina) are both good. Ribominus is much cheaper but from our lab's own experience a sample should be treated twice with the kit to completely deplete ribosomal RNA. Taking this in consideration, the price of one sample using ribozero or ribominus becomes the same, this is why we prefer ribozero. They have kits for bacteria, yeast, plant and human/mouse/rat.
Can anyone provide the sequences for the DNA oligos that should bind the 5S, 16S and 23S bacterial rRNA?
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