Performing a Plate Stamp Transfer in Benchling

Achala
Achala

Use Case Overview

This help article details the process for stamping contents from one source plate into multiple destination plates using Connect. This may be used when aliquoting material from a stock plate to individual single-use plates to prevent repeated freeze/thaw cycles, for example. This guide focuses on a 96-well plate setup but is adaptable to other plate sizes.

Prerequisite: Access to Benchling with appropriate permissions to create registry and inventory schemas.

Steps to Execute a Plate Stamp Transfer

Step 1: Setup Registry and Inventory Schemas

  • Create a Sample Schema for Source Samples:
    • Navigate to the registry settings and define a sample schema, such as "Oligo", which will be used for your source samples.

  • Configure a Plate Schema:
    • Define a 96-well plate schema or another as per your requirements.

Step 2: Configure and Create the Connect Run

  • Run Creation and Field Configuration:
    • Enter the Registry settings.
    • Select 'Run schemas' from the navigation panel and click 'Create'.
    • Fill in the required fields:
      • Name: Provide a name for the run.
      • Owner: Set to the Organization.
    • Configure the run fields:
      • Source Plate: This field should accept a single 96-well plate.
      • Destination Plate(s): This field should accept multiple 96-well plates.
      • Transfer Volume (uL): This field should accept a decimal value.
    • Click 'Next'.
    • Confirm the default access policies and update if necessary.
    • Click 'Create'.

  • Input File Configuration:
    • Initiate Input File Configuration:
      • Click the blue '+' next to 'Input file configuration'.
      • Choose a display name (e.g., “Stamp”).
    • Configure Sources:
      • Under 'Configure sources and destinations', click the blue '+' next to 'Sources'.
      • In the 'Configure lookup' modal, the 'Start from' menu will list options including each run field configured earlier, as well as 'Count field values' and 'Constant'.
        • Count field values: Counts the number of entities in a given field and uses this as a source.
        • Constant: Provides a fixed value.

  • Select Source Plate:
    • Choose the 'Source Plate' option and click 'Continue'.
    • In the next window, select the appropriate attributes. Choose 'Source Plate (96 well plate)'.
    • Use the 'Set replicates' option for source replication:
      • By constant: Replicates the Source Plate barcode a set number of times.
      • By number lookup: Uses additional information to determine the number of replicates.
    • Choose 'By number lookup'.
  • Set Destination Plate Count:
    • Select 'Count field values', introducing a second field (Schema field) to select 'Destination Plate(s)'.
    • This configuration will count the number of destination plates and replicate the source information accordingly, allowing the run to accept 1-N destination plates.
    • Click 'Continue' and then 'Insert' in the final modal.
  • Configure Destinations:
    • Click the blue '+' next to 'Destinations'.
    • Provide a name for the Destination label (e.g., “Destination Plates”).
    • In the 'Start from' dropdown, select 'Destination Plate(s)' and click 'Continue'.
    • In the 'Specify lookup attribute' page, select 'Destination Plate(s) (96 well plate)' and click 'Insert'.

 

This is what the configuration should look like so far: 

  • Configure Columns for the Input File:
    • The Source (first column) is set.
    • Click the Destination field and choose 'Destination Plates'.

  • Set the Plate Layout to 'Stamp'. Options include:
    • None: No specific layout.
    • Column interleave: Alternates columns.
    • Interleave: Alternates wells.
    • Reverse column interleave: Alternates columns in reverse.
    • Reverse interleave: Alternates wells in reverse.
    • Reverse stamp to quadrants: Stamps in quadrants in reverse.
    • Stamp: Stamps the entire plate.
    • Stamp to quadrants: Stamps in quadrants.

  • Add and Configure Columns:
    • Right-click the Plate Layout column and select 'Add new column'.
    • Right-click the new column header and rename it 'Source Plate Barcode'.

  • Click the downward arrow in the 'Set lookup' field and select 'Set lookup'.
  • In the 'Configure lookup' modal, select 'Source (Source Plate (96 well plate) → Replicates)' as the 'Start from'.
  • Click 'Add lookup step' and select 'Look up plate of container'.

  • From the 'Plate of container' dropdown, choose '96 well plate' and click 'Continue'.

  • In the 'Specify lookup attribute' page, select '96 well plate' and click 'Insert'.

  • Repeat these steps to add columns for 'Destination Plate Barcode'.

  • Add Source and Destination Coordinates:
    • Add a new column and rename it “Source Plate Coordinates”.
  • Choose 'Source (Source Plate (96 well plate) → Replicates' from the 'Start from' dropdown and click 'Continue'.
  • In the 'Specify lookup attributes' page, select 'Position'. Choose the layout option for well coordinates (down columns or across rows) and click 'Insert'.
  • Repeat these steps to add “Destination Plate Coordinates”.

The input table should now look like this: 

  • Add Transfer Volume Column:
    • Add a new column and name it “Transfer Volume”.
  • Select the 'Transfer Volume (uL)' run field as the lookup object and click 'Continue'.
  • In the 'Specify lookup attribute' page, click the box to 'Consolidate results into a single row'. This ensures the Transfer Volume is listed on each row of the input file.
  • Click 'Insert'.
  • Finalize Input Table:
    • Review and confirm that the input table configuration matches the example provided.
    • No need to apply transforms to the input file or configure the file format.
    • Click 'Update' to save the configurations.
  • Output File Configuration:
    • Initiate Output File Configuration:
      • Click the blue '+' next to 'Output file configuration'.
      • Choose a display name. If the display name matches the Input file configuration, users will have the option to generate and upload the file in one click.
    • Configure the Output Table:
      • Select 'Transfer samples' under Benchling action.
      • By default, Benchling will display one row per sample. This can be adjusted to display one row per plate if needed.
      • The default table sorting is alphabetical, but this can be changed to preserve the order of the uploaded file.
      • Under Inventory schema, select 'Use existing destinations'.

  • Configure Column Mapping:
    • Click 'Set columns' to configure the column mapping.
    • The output file can be mapped in two ways:
      • By column order: Suitable if column names may change but their order will remain constant.
      • By column name: Suitable if the order of columns may vary, but their names will remain constant.
    • For this example, select 'By column name'.
  • Add Columns:
    • Click '+ Add Column' five times to match the number of columns in your input file configuration.
  • Name each column exactly as they appear in the input table (excluding the first three columns).
  • Use the dropdown under 'Column type' to find the matching configuration:
    • Source Plate Barcode: Should follow Source: Source Plate Barcode.
    • Destination Plate Barcode: Should follow Destination: Destination Plate Barcode.
    • Source Plate Coordinates: Should follow Source: Source Plate Coordinates.
    • Destination Plate Coordinates: Should follow Destination: Destination Plate Coordinates.
    • Transfer Volume: Should follow Amount: Transfer Quantity: uL.
  • Finalize and Save:
    • Ensure the final column mapping looks correct.
    • Click 'Done'.
    • For this use case, there is no need to change the delimiter (set to comma by default) or Data locale.
    • Click 'Update' to save changes.

Step 3: Testing the Run

  • Prepare the Notebook:
    • Open a blank notebook entry.
    • Add a plate creation table and the Plate Stamp Run.
  • Fill the Source Plate:
    • Populate the source plate with entities. For example, fill the source plate with Oligo entities using the schema defined in Step 1A.
  • Populate Run Fields:
    • Populate the run fields with the relevant data.
    • Click 'Create' to set up the run.
  • Generate the Input File:
    • Click 'Generate' and choose one of the following options:
      • Generate input file: If the transfer is being performed by an instrument, this file can be uploaded as instructions.
      • Generate and send to output: This option will generate the input file and also process the transfer step in Benchling.
  • Process the Run:
    • Once the input file is generated, click 'Process all' to complete the run.
  • Verify the Outputs:
    • Expand the Run outputs. The Stamp results should look like the configured output.

Additional Notes

This procedure can be customized to fit different laboratory and protocol needs by adjusting the schema settings and configurations as necessary.

Conclusion

Following these detailed steps will allow you to efficiently aliquot samples using the Benchling platform, optimizing your lab's throughput and sample integrity.

 

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