Extraction Guide

Introduction

Once you have taken the time to setup your inventory, tests, and protocols you are now ready to process samples for extraction. This guide will teach you how to create a batch of samples with their corresponding assays and extraction protocol.

Creating Batches

Creating DNA-qPCR Batch

Step 1 - Creating a batch of samples for extraction is the first step to creating paperwork. To create a batch, click on “Extraction” and select “Create Batch”.
Step 2 - Set the Name as “DNA-qPCR Batch” and set the Number of Samples as “10”. Leave “Add Negative Control” checked as this will create a negative-control sample. This means in total, you will have 11 samples.
Step 3 - Next let us set the Lab ID as “AAA”. The lab ID is used to distinguish a batch and its corresponding samples.
Step 4 - Then we will select the panel “DNA in qPCR Panel”. Click on “Extractions” and select “DNA Extraction Protocol” as the extraction protocol for this batch.
Step 5 - Click on “Create Batch”.
Step 6 - By doing so, you will now be able to modify each sample of the batch.

Modifying Samples In DNA-qPCR Batch

Step 1 - Our recommended first step in modifying sample is to assign each sample a sample ID. The lab ID is auto-generated for the sake of internal management for each batch. But the sample ID is used to directly identify the actual sample such as the name of the tube it came.
Step 2 - The fastest way to assign each sample a sample ID is to click on “Insert ID's” and then copy/paste your list of ID's from your documents such as an Excel spreadsheet. Check to make sure there are no empty rows and then click on “Populate”.
Step 3 - In this case, we will populate our samples with “dna-qpcr-1” to “dna-qpcr-10”.
Step 4 - Save your sample ID's by clicking on “Update Sample ID's”.
Step 5 - Should you wish to change the number of samples click on “Reset Samples” and enter the new number of samples you wish to have in this batch. Let us change the number of samples to 13 which means there will be 14 total samples including the negative-control sample.
Step 6 - Once you click on “Confirm” you must then insert the sample ID's once again.
Step 7 - Because of this change we will populate our samples again but with “dna-qpcr-1” to “dna-qpcr-13”.
Step 8 - We must then click on “Update Sample ID's” once again.
Step 9 - Let us say that the first sample with lab ID AAA-1 only requires “Assay 1”.
Step 10 - To modify this specific sample click on the blue tube icon and uncheck both “Assay 2” and “Assay 3”. Click on “Update & Edit Quantity.
Step 11 - Notice how the sample is highlighted yellow and that there are warning signs next to the data for the batch. This sample has been flagged as an anomaly since it does not contain all assays specific to the chosen panel. This simply serves to warn you that not all samples will share the same exact assays as the panel you have chosen for this batch.
Step 12 - Next, let us preview the entire batch by clicking on “Preview”.
Step 13 - If you are satisfied with the results, you can go ahead and click on “Print Paperwork”.
Step 14 - By doing so, a new web page will be produced for you to print it. If the styling does not appear in the printed page, refresh the page and press the button again. Remember to close the print page before navigating back in the website.

Creating RNA-qPCR Batch

Step 1 - Let us make our second batch which only contains assays for RNA in qPCR.
Step 2 - Click on “Extraction” and select “Create Batch”.
Step 3 - Set the Name as “RNA-qPCR Batch”, Number of Samples as 5, and Lab ID as AAB.
Step 4 - The Panel selected will be “RNA in qPCR Panel” and the Extraction selected will be “RNA Extraction Protocol”.
Step 5 - Click on “Create Batch” and populate the sample ID's with “rna-qpcr-1” to “rna-qpcr-5”.
Step 6 - We must then click on “Update Sample ID's”.

Creating DNA-PCR Batch

Step 1 - We will create a third batch that is for DNA in PCR.
Step 2 - Click on “Extraction” and select “Create Batch”.
Step 3 - Set the Name as “DNA-PCR Batch”, Number of Samples as “2”, and Lab ID as AAC.
Step 4 - The Panel selected will be “DNA in PCR Panel” and Extraction selected will be “DNA Extraction Protocol”.
Step 5 - Click on “Create Batch” and populate the sample ID's with “dna-pcr-1” to “dna-pcr-2”.
Step 6 - We must then click on “Update Sample ID's”.

Creating All Assays Batch

Step 1 - We will create our fourth and final batch that is for all 5 assays we created.
Step 2 - Click on “Extraction” and select “Create Batch”.
Step 3 - Set the Name as “All Assays Batch”, Number of Samples as “15”, and Lab ID as AAD.
Step 4 - The Panel selected will be “All Assays Panel” and the Extraction selected will be “Total-nucleic Extraction Protocol”.
Step 5 - Click on “Create Batch” and populate the sample ID's with “all-1” to “all-15”.
Step 6 - We must then click on “Update Sample ID's”.
Step 7 - Your list of batches should look similar to the image below.
Step 8 - Confirm that all your batches are the exact same as the ones in this tutorial. When you have confirmed, go to each batch and click on the green button labeled “Extracted”. By doing so, you inventory will be updated based on the amount of reagents and tubes used.
Step 9 - Extraction Reagents Before Processing Batch.
Step 10 - Extraction Reagents After Processing Batch. Notice how units have changed to μL.
Step 11 - Tubes Before Processing Batch.
Step 12 - Tubes After Processing Batch. In this tutorial, we processed 39 samples in total. As you can see 1 QIAmp Mini Spin Column is used per sample. We originally had 50 but because we had to use 39 for the 39 samples, we now have a remaning number of 11 QIAmp Mini Spin Columns.

Conclusion

You are well on your way to creating a completed document for PCR paperwork! Once your samples have been extracted, you will now be able to process each sample for PCR. Read the PCR Guide next!