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PCR Planning and Inventory Check Tool
PCR Planning and Inventory Check Tool

Plan PCR plate layout and choose PCR materials from inventory

Written by Chris Lamkin
Updated over a week ago

This tool uses the PCR Reaction Table output by the j5 protocol generator to generate plate maps for left primer, right primer, and template sequence plates. The tool allows you to manually assign the PCR reactions to locations in a PCR plate or use our algorithm to automatically assign the PCR reactions to locations in a PCR plate. The algorithm will assign locations in a way that optimizes the PCR reactions when using zone gradient thermocycler.

Input: DNA Assembly Report

Output: PCR Plate Map, PCR Material Inventory Lists, PCR Material Order Lists

You can find more detailed definitions of the terms mentioned in this article in the glossary.


  • Input DNA Assembly Report (Required)

You can find the PCR Planning and Inventory Check tool under Tools > Tool Library. Click ‘Launch Tool’ to start using the tool.

The tool consists of three steps: j5 PCR Selection, Plate Configuration, and Inventory Check.

Step 1: j5 PCR Selection

Begin by selecting (or uploading) a DNA Assembly Report.

Once selected, a list of PCR reactions associated with the selected assembly report will appear. Choose which PCR reactions you would like to run. A green checkmark indicates that the sequence exists in inventory. Click "Next" when you have made your selection.

Step 2: Plate Configuration

Begin Step 2 by selecting a plate format for the PCR Plate. We currently support 96 and 384 well PCR plates.

Next, determine the layout of your PCR reactions. By default, we will distribute reactions based on the temperature information from the selected assembly report. However, other distribution options are available, including disabling temperature zones. Click "Next" to proceed to the next step.

Step 3: Inventory Check

In this step, users have the option of selecting PCR materials (primary templates and primers) that exist in inventory (have samples/aliquots on plates or in tubes in the system).

Either choose aliquots for the Primary Templates, Forward Primers and Reverse Primers manually by clicking "Select Aliquot":

Or automate sample selection by clicking the dropdown below the section description, selecting "Last Modified" or "Fewest Plates" and then clicking "Automate Sample Selection". "Last Modified" will choose samples most recently updated or created, while "Fewest Plates" will choose a set of samples from the fewest amount of plates.

PCR Materials that are not selected from inventory will be added to Order Lists which will be output by the tool. These order lists can then be used to order the missing materials from the BioShop or Online Ordering tool.

Finally, input names for the data that will be output by the tool (or use default names) and click "Submit".

Once complete you can proceed to the Bioshop/Online Ordering tool to order any missing PCR materials or use the Run PCR tool to generate a PCR Worklist.

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