Single vs. Bulk

You can register plasmids in two ways: single plasmid registration or in bulk.  

  1. The single registration process works well for registering 3 or less plasmids. You'll import your plasmid map, fill out metadata, register, and then create new batches.
  2. The bulk process works well if you need to register many plasmids.  You'll import metadata and batch information, import plasmid maps, and then register. 

Single Plasmid Entity Creation and Registration

  1. Open a project folder
  2. Toggle to the Inventory Section.
  3. Click “+” and Import DNA. Drop in your plasmid file. Note that we first import all entities in the Inventory before promoting them to the registry
  4. Toggle to the Metadata Tab and set schema to Plasmid. Depending on your organization's preferences, the 'Plasmid' schema name might be slightly different (i.e. Construct, "Type A" Plasmid) 
  5. Fill in values for metadata like for each field

There are a few fields that are Part Links. Select Autofill Part Fields to link any Part links to your plasmid map. Identified parts will show up as links. See below for how you can create new parts straight from your plasmid map. 

If everything looks good, hit the Register button at the top of the metadata page. 

In the Register modal, you'll see a few options for generating your ID.

  1. Generate new registry IDs: Benchling will keep the name of your files, but also give you a registry ID. Note that all names must be unique so you'll hit an error if the file name already exists in the registry.
  2. Generate new registry IDs based on entity names: Benchling will generate an ID based on the entity name (e.g. DNA002 would be converted to p002). You likely won't use this option.
  3. Generate new registry IDs and replace name with registry ID: Use this option if you want to make the Registry ID the Name of the entity. Benchling will give you the next ID and then replace the name with the ID. Use this option if you're using a "throwaway" name for your entity.

Depending on the configuration for the 'Plasmid' schema, you will either be able choose from one of the above options or be limited to only one pre-designated option.

Creating Batches Individually

Each entity in Benchling can hold multiple batches. These repesent the actual samples of your constructs. For example, after you've done a Maxi prep, you'll want to create an actual batch of a plasmid. To do so:

  1. Search and open the Construct entity. 
  2. Toggle to the Batches tab and click on the "+" sign next to Batch.
  3. Fill out the appropriate information.
  4. You can now use this batch ID on your tube. Remember that you can also @ mention batches in your ELN.

Bulk Plasmid Registration

You may often have multiple files that need to be registered. In this case, you'll need to use an Excel template to prepare your data.

You will first import the metadata for these plasmids in bulk. To do so, prepare an Excel template with the data. 

Important Notes: 

  1. The Name column will have to match the name of your plasmid files from Snapgene, Geneous, or other softwares.
  2. The csv should have batch fields columns. If you've made an actual sample of the plasmid, you should fill these in now. If not, you can hold off on inputting this data.
  3. The csv should have a column for Bases. You'll keep this blank for now since we'll reimport our plasmid maps in a later step. 

Next Steps

  1. Open your project folder.
  2. Toggle to the Inventory Section. 
  3. Click “+” and select Import Entities
  4. Select Plasmid (or similar name)  from the schema dropdown. Click Next.
  5. If you want to create batches at this time, we suggest you check off the box Create Batches with Entities. Benchling will create batches as the same time as entities 
  6. If you are using sample management [ENTERPRISE ONLY] and would like to simultaneously create a container and deposit into a Sample Management Location (i.e. Box), then select Create Containers with Input Batches and designate the container schema.
  7. In the following window, select Raw Text option from the dropdown
  8. Go back to your Excel template and copy out the data. Make sure to include the headers. Paste this into the Import modal. Click Next.
  9. Benchling will map the column headers to schema fields in the registry. If you used the above template, Benchling will autodetect the correct fields. Once confirmed, click Next. Note: if you selected the create batches, Benchling will map Batch fields from the Excel sheet.
  10. In the next modal, Benchling will check for errors. If there are errors, you can select the files and click Remove Files or may be required to make modifcations in your Excel sheet. Note: the most common error will likely be that you're missing the Bases column from your Excel sheet. Again, this should be blank but Benchling expects a column header for Bases.  
  11. Once complete, hit Import. These entities and batches should now be in the project you imported them to. Find the project and expand the view by selecting the Arrow on the top right of the side panel. If you click into an entity, you'll notice that you won't see any sequences for that entity. 

Re-importing your Plasmid Sequences

  1. Now it's time to import your sequence map to the Benchling registry. Click the "+" sign and then select Reimport DNA Sequences. 
  2. In the new modal, you can now drag and drop in your sequence files. You need to make sure that the file name is the same as the entity name in Benchling. Once you drop all the files, select import.

Registering your Plasmids

Now just Register your plasmids by expanding the side panel, selecting your plasmid entities, and then hit register.

Bulk Update Plasmid Entities

  1. If you need to edit existing Plasmid metadata, you can do so by finding the specific construct through the registry and editing fields. If you need to do this in bulk, you can do this by using a spreadsheet importer.  
  2. You can use the same template as before but exclude the Bases column.
  3. Again set up your template with the appropriate data. You should include the Registry ID in the Name column. Note: you can copy out registry IDs by selecting in the Export button in the registry.
  4. Go to the registry, select the "+" sign, and select Update Entities. In the new window, select Plasmids as the schema to update
  5. Follow the import steps as outlined earlier in the previous section.

Creating or Editing Batches in Bulk

If you need to create new batches indivudally, refer to the Creating Batches Individually section above. If you were bulk importing plasmid maps, but didn't create batches during this process, you can create them afterwards too. Follow the steps below: 

Bulk Import Batches

  1. Again set up your template with the appropriate data. You should include the Registry ID in the Name column. 
  2. Go to the registry, select the "+" sign, and select Import Batches. In the new window, select Plasmids (or similar name)
  3. Follow the import steps as outlined earlier in the previous section. Note: Benchling will ignore all non-batch fields in the import modal. 

Bulk Update Batches

  1. If you need to update batches, follow the same instruction as in bulk import batches usng the same csv template, with a few differences:
  2. Navigate to the Registry, click on the + icon and select Update Batches
  3. Make sure to include the batch ID in the spreadsheet for update. Include a column/header in the spreadsheet corresponding to each field you would like to update.

Part Links

Creating New Parts from Plasmid Maps

Right click on a selection in your Plasmid map. Note: Make sure that your selection does NOT partially overlap with an existing annotation. Select Create New Part and then select the specific part type you want to create.

Give your new part a name.

Notice the new integration field filled in the Metadata section for your part. Once all parts are defined, you can go ahead and register your parts!

 

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