Description

This package contains a macro to reassign the libraries in a plate based on the indexing steps.

This package contains the following entities:

  • A content type: 
    • DNA Library.
  • A macro: 
    •  Store libraries in plate: With two steps of type Edit content.
  • A location type: 
    • Plate 96 well: With 8 rows (alpha-numeric) and 12 columns.
  • Five custom fields on Content:
    • Barcode – I7: A field of type dynamic choice on the value table DNA index.
    • Barcode – I5: A field of type dynamic choice on the value table DNA index.
    • 96 well id: A field of type Short text, that is automatically calculated based on the content’s position in a location, in the format columnRow (ex. 01A)
    • Library plate: A field of type dynamic choice on the value table Location.
    • Automatic move: A field of type Checkbox.

How to use the package

Pre-requisites

  • The latest MiSeq package available in the Package Browser module should be imported before importing this package.
  • A workflow has to be available with a Protocol of type NGS: Library preparation
  • Additionally, in order to run an NGS workflow:
    • A requestable must be created.
    • A DNA index set must be created in order to use the workflow.
    • A Plate index design must be created in order to use the workflow.
    • A sequencing setting must be created in order to use the workflow.

Configuration

Protocol

The NGS: Library preparation protocol (pre-requisite) can be completed with the addition of the Store libraries in plate macro. To do so, an additional step of type Link content should be added after the index allocation step. The macro restriction should be set to the Store libraries in plate macro and this macro should be set to run on start of step.

Fields:

The field 96 well id can be restricted to the content types that enter the Library preparation step of the NGS: Library preparation protocol. The value expression can be changed to fill in a row-wise value instead of the default column-wise. The field has been configured to return column-wise to facilitate the move of samples from the list view to the plate view of the Content selection step while maintaining the same position of the samples.

Macros:

The macro Store libraries in plate is used to automatically move libraries to the correct position in the plate, based on a selected location. If the field 96 well id should also be filled out on the DNA Library contents, an additional edit step has to be added to the macro and the field’s default value expression should be executed in this step.

Usage step by step

  1. In the Locations module, create two plates of type Plate 96 well.
  2. In the Content module, create samples and add them to the first plate.
  3. Send the samples to the workflow.
  4. Start a protocol run of the NGS: Library preparation protocol.
    1. Move the samples into the correct place on the plate in the Content selection step.
      1. You can make use of the field 96 well id to sort your samples and drag them onto the plate if you enable the checkbox Use checkboxes to drag samples.
        (warning) If the value expression of the field 96 well id is changed to fill in a row-wise value, you need to disable the Fill by Column checkbox.
        (warning) This only works if there are no missing samples in the plate. Missing samples will be replaced on the plate with the next in line.
    2. In the Index allocation step, select a plate design to fill in the indexes for the created DNA libraries.
    3. In the Store libraries step, the Store libraries in plate macro will start automatically. Fill in the Library plate field with the second plate. The macro will then move the libraries into the correct plate position of the selected plate based on their position in the plate of the previous step.

Where to Look Next

These references have further information on how to configure or use the package contents after the initial installation and integration.

  • Content Management > Content Types
  • Content Management > Locations and Location Types
  • Workflows > Workflow Management
  • Electronic Lab Notebook > Protocols
  • SLIMS-NGS > DNA Index Sets
  • SLIMS-NGS > Plate Index Designs
  • SLIMS-NGS > Sequencing Settings
  • Miscellaneous > Fields > Custom Fields
  • Miscellaneous > Macro

This package is also available in combination with a protocol that has the macro preconfigured in it. This package can be imported in the Workflow Management module into a workflow by clicking on “Import protocol.” Contact your SLIMS administrator for additional help.