Template for bacterial samples

[Cajac102]

Hello everyone,

I would like to suggest a template for bacterial samples that covers standard parameters about the laboratory growth conditions. These conditions (such as medium, growth temperature, and growth phase) can have large impacts on the proteome and are commonly reported in papers. There already exists an ontology that covers a lot of the necessary terms, it would be great if this ontology could be supported in SDRFs as well. Based on this ontology, I suggest to use these columns in addition to the default ones:

• characteristics[medium]: Medium the culture was grown in/on
• characteristics[medium supplements]: Additional substances added to the medium, most often antibiotics (might be merged into characteristics[treatment]?)
• characteristics[temperature]: Temperature in which the culture was grown in
• characteristics[optical density]: Optical density (OD600) of the culture
• characteristics[growth phase]: In which growth phase the culture was in at time of harvest
• characteristics[mutant]: describes if/how the sample was genetically altered (plasmids, CRISPr)

Optional ones:

• characteristics[aeration]: Describes if the culture was grown under aerobic/anaerobic conditions
• characteristics[pressure]: Pressure in which the culture was grown in
• characteristics[pH]: pH in which the culture was grown in
• characteristics[growth rate phenotype]

Kind regards,
Caro