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Updating References

Updating-References.Rmd

Freezer names

SampleDB requires freezers to be entered into the system before samples can be uploaded. Every location should have 3 levels of information.

  • The top level is the FreezerName. This is the freezer identifier.
  • The second and third level can be used as coordinates to identify samples on a shelf.

Every sample will need these three levels of information during an upload. The exact first, second and third level information can be found in the database under References > Locations. If you are uploading samples, it is recommended that you search for your freezer in the locations table to get the exact position information you need for your upload.

Specimen Types

Establish and add common specimen types under References > Specimen Types. Every uploaded sample must have an associated specimen type.

Specimen types should be easy to understand. Below are some examples:

Specimen Type Description
DNA (WB) Extracted DNA from whole blood
DNA (DBS) Extracted DNA from DBS
DNA (RDT) Extracted DNA from RDTs
DNA (MG) Extracted DNA from midguts
Plasma (WB) Plasma from whole blood
Serum (DBS) Serum from DBS

Adding a study

Pick a Study Title, Study Description, Lead Person, and Study Short Code for any new study entered into SampleDB. Before adding new studies be sure to check that study does not already exist, otherwise you will have multiple names for the same study. You can have different types of specimens from the same study and should use the same study name.

  1. Study title should be the name of the study, ie. “LLINEUP2” or “IMMRSE-U”.

  2. The study short code will need to be included in the CSV whenever samples are uploaded. For example, a good study short code for PRISM Border Cohort would be PBC. For IMMRSE-U, use IM. For LLINEUP2, LN2.

  3. The study description should be as specific as possible, so that if someone unfamiliar with the study is using the database they would understand how the samples were obtained. “IMMRSE-U” could be described as “DBS collected from 30 malaria reference centers for malaria genomic surveillance from 2022-2025”. “LLINEUP2” could be described as “DBS collected from repeated cross-sectional surveys at 64 sites as part of a cluster-RCT trial of bednets from 2020-2023”.

  4. The lead person should be specific, so that if someone is referencing this database in the future, they know who to contact.

***The above steps must be done before attempting to upload plates for a study.***