I performed pyrosequencing of soil samples that were previously subjected to some stress conditions for specific time period. Results obtained show clear difference between control and experimental soil sample.
I want to know if data publishing will require some supporting techniques? or validation of th data is required by some other method too?
or pyrosequencing is enough for establishing some conclusions?
Dear Maliha,
In the link you find different kinds of illustrations to present data with:
https://en.wikipedia.org/wiki/Pyrosequencing
You can validate the data by performing qPCR of the organisms/DNA sequences that are showing significant changes in your control and experimental samples.
SD
Our lab group just submitted a paper that included Illumina sequencing results from a soil microbial analysis in response to soil amendments. We included metadata such as plant growth response, disease severity and pathogen initial inoculum changes in response to the amendments. Illumina sequence data explained findings from metadata. I think it would be helpful if sequencing data can be supported with metadata.
Data validation using qPCR
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174806/
Hi Maliha
By validation I guess you mean confirming whether the difference between samples/treatments is consistent irrespective of the method used to quantify a particular parameter. In that case real time PCR or metagenomics (amp reads to binned genomes) would be suitable validation tools.
Experimental design is one of the most important considerations though. It is common that people neglect replicating samples within treatments which means that they are unable to say A is significantly larger/smaller than B. If there is no replication and the objective is to say that something differs from a control (for example) there is no point in validating population abundances within single samples - it is better to repeat the experiment with adequate replication.
I hope this is useful
Add a positive control (like you do with all other scientific techniques). Like a synthetic community with known composition of either, 16S clones, amplicons or genomic DNA or whole bacteria. There are several available, or you could make your own with the players of interest unsually associated with your ecosystem of interest. Generally this is nog asked for by reviewers, but it would strengthen the conclusions (and the whole field) if this would be consideren mandatory.
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