When we receive samples, whether they are DNA, RNA or Premade libraries, they first undergo our quality control (QC) assays before being processed by the Library Preparation Team or Sequencing Team. Performing these assays allow us to make informed decisions about how to optimize the library prep/sequencing process in order to provide our customers with the best data possible.
At OGC we have a dedicated QC technician who deals with all samples, from receipt to passing on to the Library prep/sequencing team. We aim to have a two day maximum turnaround time for the checking of samples, after which, if any issues arise, the customer is contacted by their project manager who will explain the issues and offer advice on how to proceed.
The first step of the QC process is to receipt the samples. For this process to go well, customers should only send their samples after they’ve received a Project Number. This means the samples have been entered into our Laboratory Information Management System (LIMS) and that when they arrive we have all the information we need.
Including sample type, desired workflow, sequencing notes, how to label them and more. Without a Project Number, a sample-specific LIMS ID will not have been generated, meaning we are unable to label samples or correctly allocate freezer space for them. See our submission requirements.
Along with attaching the correct Project Number to a sample, we also like samples to have been stored correctly. If you have more than eight samples, we ask that they are stored in columns in a 96-well plate, either skirted or semi-skirted. If you have eight or less, sending them in recommended tubes is fine e.g. 1.5mL Eppendorf’s. Please also securely seal your samples with a suitable lid, this minimizes contamination occurrence during transportation. We also request clear labelling, matching the customer sample submission form sent to the project manager and/or included in transport. See submission requirements.
In 2016 we dealt with over 26,000 samples, for more than 840 projects! However the time saved by correct labelling and packaging would allow us to complete so many more in 2017.
During the QC stage, the quantity and quality of a sample is measured. The type of assay performed depends on sample type and the workflow it will be entered into. The more starting material there is, the higher the chances of a successful prep. A general rule for DNA and RNA samples is that we require 1ug of starting material in the appropriate volume for the given workflow. We also like the starting material to be of a good quality, which is another factor that decides the success rate/levels of library prep. Examples of high quality DNA/RNA are at the end of this article.
There are times when a high quality sample is impossible to obtain, which is why we offer workflows made specifically for these situations.
Table 1 summarises the optimal input masses in required volumes for some of the workflows that we provide, while the figures show samples with varying degrees of degradation.
Author: Benjamin Carpenter