Dear researchers,
We have a set of samples of which we would like to perform RNAseq on the determine the transcriptome.
On the other hand we would like to find out what bacteria can be found in the place where we took the samples.
I was wondering is anyone has experience with isolation both the 16S rRNA for the microbiome and the mRNA for RNAseq analysis.
Thank you in advance!
I think it is possible but you need to be more specific about choice of samples for both experiments
Yes, you can determine the transcriptome and microbiome from the same sample. You can see this paper on comparative analysis of the transcriptome and microbiome from the same samples.
Determine transcriptome and microbiome from the same sample is perfectly possible.
Some interesting programs to help you do this are:
MetaQUBIC
https://doi.org/10.1093/bioinformatics/btz414
HUMAnN2
https://www.nature.com/articles/s41592-018-0176-y
QIIME
http://qiime.org/
Megan
http://ab.inf.uni-tuebingen.de/software/megan6/
But many other programs are available.
You can extract DNA and RNA from the same sample if you want to use DNA for microbiome and RNA for transcriptome. You could also amplify the 16S rRNA from the RNA fraction after conversion to cDNA.Or just 'keep' the rRNA in your transcriptome (it will be most of your sequences anyway if you don't use a kit to reduce the number of rRNA or amplify the mRNA) and use that fraction to determine community structure. Many options, really depends on your scientific questions.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA