Setting up barcoded runs using strain or compound source plates

1. Benefits of Barcoded Growth plate setup

In the barcoded growth plate setup, a growth plate is linked to a strain or compound source plate and a growth protocol defining growth conditions such as temperature and number of runs at the setup bench using barcodes.

This has several advantages:
- It speeds up the growth setup procedure including the time otherwise spent on configuring the growth protocol at the ACCESS robot.
- It links the plates to a file in the DB by unique barcodes, this prevents errors such as running a plate under the wrong name.
- It automatically annotates with informations such as strains and drugs used in each well in only a few steps.

2. DB_interface main window

1. Click on Setup_Plates, a new window will open

3. Setup_Plate interface

1. Select user
2. Select Project
3. Select 1 source plate for 1-4 96 well plates (i.e. for one strain plate and 4 drug conditions) or select 1-4 source plates for 1-4 96 well growth plates (i.e. for 4 strain plates with individual drug conditions)
4. Check or change created plate size
5. Select the type of source plate
6. Select the type of screen
7. Refine growth plate name by adding the source plate name, project name, custom string or the drug/strain name. Drug and strain names can be shortened using Truncate_to_n_Chars > 0
8. Scan the first source plate position barcode (SP-pos-1)

4. Scan the source plate position barcode

- Scan the source plate position barcode and press enter
- A new window will open to scan the unique source plate identifier

5. Source plate barcode

1. Scan the unique source plate barcode
2. Click on the button Scan

6. Scan the first growth plate position barcode

- Highlight text and scan the barcode
- Press enter
- A new window will open to define the unique growthplate barcode

Barcode composition and explanation:
gp: growth plate
stn-yourfavoritestrain-stn: annotates the plate with "your favorite strain"
drg-yourfavoritedrug-drg: annotates the plate with "your favorite drug(s)", for double drugs use drg-drug1:+:drug2-drg
pos-1, pos-2, pos-3 or pos-4: growth plate position ( see note below

Notes:
- In the option 1 source plate for 1-4 growth plates the pos-1, pos-2 etc are used to indicate the 4 growth plates connected to one source plate. These growth plates can each have a different drug or a different strain.
- In the option 1-4 source plates for 1-4 growth plates, the source plate at position 1 will be connected to the growth plate at position 1, the source plate at position 2 is linked to the growth plate at position 2 etc.

7. Define the unique growthplate barcode

1. Scan the prepend code to make the barcode unique
2. Scan the numerical barcode
3. Click Scan button

Note: this barcode must be unique! If the barcode already was entered into the DB try to prepend another unique string of characters.

8. Define media and drug concentration

1. Select growth medium
2. Select diluent
3. In drug volume enter the drug concentration (double drug not yet possible, correct after growth plate creation see below)
4. Enter units in the drug_vol
5. Click on Create Growth Plate button

A new interface will now open to select the Growth protocol.

9. Select Growth protocol

The growth protocol contains all pertinent information such as:
-temperature
-measurement type
-number of runs
-reference well
etc

1. Click on the protocol
2. Click on Select button
3. If the list does not display the correct growth protocol, change plate type screen

10. Growthplate status

Check the growth plate status and look for possible error messages.

11. Verifying the created Growth Plate Layout:

- When first starting out using the barcoded plate setup, it is advisable to verify that the growth plate layout was created correcty.
- For double drug annotation, the concentrations and units cannot be annotated in the barcode setup interface, use the steps below to add this information.

Viewing Growth plate layout when still in the Setup_plate interface

1. Highlight a growth plate name
2. Click on View/Edit G Layout

12. View and modify growth plate layout from the DB_interface main window

1. Click on View and Define_Plate Composition, a new window will open

DB_Plate_Layout interface

1. Set the plate type to the type of the created growth plate
2. Enter growth plate name (or part of the name)
3. Click Select Plate_Name or Layout from DB, a new window will open

13. Select_Plate_Name interface

1,2. Refine search if too many plate names are returned
3. Press Refresh_Plate_List
4. Highlight plate name
5. Click Select

14. DB_Plate_Layout interface - Plate Composer tab

1. Growth plate layout is loaded in the Plate Composer View
2. Press edit in Spread_sheet view, a new window will open

15. Copy Table to Clipboad interface

- Edit Drug_Name (1), Drug_Conc (2), Conc_Units (3) and Strain_Name (4) and Strain_Background (5) as necessary.
- For double drug combinations enter values of drug 1 and drug 2 separated by :+: ( i.e. methotrexate:+:folinic acid, 250:+:60, uM:+:ug/ml)
- Click Update (6) and Done (7)

Note: look at Well Annotation instructions for a more detailed description of this interface.

16. DB_Plate_Layout interface - Plate Composer tab

Press Save_plate_defn to DB to update the growthfile!!!

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