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Sample Collection > DNA Extraction > Sample submission > Downstream analysis

Sample collection 

Stool collection kits are assembled by OCMS and shipped to clinical sites to be distributed to study participants. Participants are provided with step-by-step instructions on how to collect their sample and package the sample safely. We also have a standard dietary questionnaire which can be provided which documents the dietary trends of the participant. 

We have set a Royal Mail Medical Tracked 24 Hour Service for the direct return of samples from the participant to the OCMS. Samples are posted in standard Royal Mail red post boxes in UN3373 Category B Biological Substances boxes. Samples are tracked from when they are first scanned by Royal Mail ensure all samples are traceable once in the system. This also means that only those kits returned to OCMS are charged postage.  

DNA Extraction 

We routinely perform DNA extraction from clinical samples for microbiome analysis by either 16S or Shotgun metagenomic sequencing. We have tested commercially-available extraction kits and homogenisers in order to benchmark our DNA extraction approach. Further details of our optimisation experiments can be found in our OCMS blog. As standard, each extraction run includes a commercially available microbial community standard in order to validate each extraction run. 

Downstream analysis 

Samples can then be organised and submitted for sequencing at the Oxford Genomics Centre. Downstream analysis by our Bioinformaticians may inform more detailed analysis and further experiments, for example, in our Gnotobiotic Facility