2023-05-04

This is Audrey's DBGI daily open-notebook.

Today is 2023.05.04

Todo today

Have a look at the DBGI discussion forum

- https://github.com/orgs/digital-botanical-gardens-initiative/discussions

Doing

Paused

Done

Notes

Tutorial

DBGI Workflow : from the creation of an DBGI_ID to the LC-MS analysis

In order to use the workflow you will need to have the following account / application : directus, Avery, Qfield, Inaturalist,

DBGI Labelisation

Principe

DBGI_ID will allow you to link the plant, the extract and analysis.

DBGI_ID can be composed of :

The plant identification helps you to connect all the plant metadata (localisation, species, genus).

The extract code is corresponding to the stock vial obtained and conserved in freezer.

The vial code is referring to the vial analysed. Usually around 150 µL of stock extract is taken and transferred to a vial for analysis.

At each step you will need to print labels to identify falcon or vials.

Pratical

a. Creation of an account on directus

b. Implementation of the dbgi_ID list using Basics protocol.

c. Download the .csv file with your new dbgi_id

d. Add the following column

d. Label creation using Avery.

Import the corresponding template to avery. Then import the dbgi_ID list.

For plant sample select the column dbgi_ID ; modify the QR code according the dbgi_ID (check QR code with a QR code reader)

For vial label use the vial label columm and create an associated QR code

e. Print label Sample label are print on L4732 sheet Vial label are print on L4731 sheet

f. Labelling falcon tube/vial + protect with scotch tape

Plant's collect

a. Before collecting : provide for sufficient falcon tubes with DBGI-SPL-ID

b. Qfield software (follow the protocol section 'utilisation of Qfield' http://www.dbgi.org/dendron-dbgi/notes/h33m4gr8eny7li4yhlxotdb) during collection

c. The transfert of the data collected on iNaturalist is automatic

Extraction

(extraction section : http://www.dbgi.org/dendron-dbgi/notes/mpboa8wpvhpygf5fw4o9v11/)

100 µL in one vial for analysis LC-MS/MS + one vial with ~XX µL in the freezer

LC-MS analysis

a. Preparation of the samples list

b. Analysis

Datatreatment

for datatreament follow the link

Todo tomorrow

Modification of the Dbgi name dbgi_00000_01_01 (n° vial)

Today I learned that