Create and register DNA and AA sequences in bulk

  • Updated

If you're looking to register 3 entities or less, please refer to this article on how to create and register a single entity. For registering more than 3 entities at once, the following article will explain how to register these entities, as well as how to import their metadata and DNA or AA maps.

Creating a spreadsheet with the entity data

The data related to entities you want to import will need to be formatted before being uploaded to Benchling, this can be done through a spreadsheet template.

Important notes for the spreadsheet template:

  • The spreadsheet needs a name column. The values in the column need to exactly match the name of your DNA / AA sequence files from Snapgene, Geneious, or other softwares. See the file formats supported by Benchling here.

  • The spreadsheet should have a column for bases or amino acids. Keep this blank for now, the sequence maps will be reimported in a later step. 

Importing entities from a spreadsheet

To import entities into Benchling in bulk, navigate to the Registry tab (9 dot symbol) on the left navigation bar > + > Import Entities. Select the schema of the entities you're importing and mark the check box if your DNA is circular, then press Next.

Note: If you're using the Inventory application and would like to simultaneously create a container and deposit it into a Location (i.e. Box), then select Transfer entities to new or existing containers and designate the container schema.

Now add your spreadsheet, you can either import the full spreadsheet or copy and paste the fields from your spreadsheet template into the raw text box. Please ensure that you include the column names. Once this is done, select Next. In the next menu ensure that the column names pulled from your spreadsheet match the column type fields. Once they're matched press Next, Benchling will now check for errors. If no errors occur, press Import. Your entities will now be viewable in the Registry.

Note: The most common error will likely be that you're missing the Bases column from your spreadsheet. Again, this should be blank but Benchling expects a column header for Bases or AA.


Reimport your DNA/AA sequences

Now it's time to import your sequence map into the Benchling Registry. Within the Registry click + and select Reimport DNA or AA Sequences. 

In this menu, you can now drag and drop in the sequence files, and the file name must be identical to the entity name in Benchling. Once you add all the files, select import. Each sequence file should also contain only one sequence per file, as Benchling will generate an error if multiple sequences are found in one sequence file. 

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