The Ultimate Guide to Fast Genome Sequencing

Your grant funding expires soon, your clinical trial deadline is fast approaching, or maybe your research is at an impasse because you’re lacking critical genomic data to continue. Whatever time-sensitive pressures are weighing on you, we have some great tips to keep your project moving at maximum speed.

Define Your Research Clearly

This might seem like a no-brainer, but clearly defined research objectives reduces the time needed for follow-up emails and clarification.

Establish Your Sequencing Needs

In your initial conversations, make sure to include:

• What genus/species you’re researching
• Link to a reference genome or determine if de novo assembly is a possible solution for your research goals
• A brief description of what your research entails
• If you have a deadline or other specific delivery requirements

Quality Samples Yield Quality Results

Good results stem from submitting high quality samples. Our detailed sample submission guidelines are a great place to start, but here are a few extra pointers.

Cell Counts

When submitting cell pellets and PBMC, the minimum cell concentration we need is 5*10^6 cells/mL in order to yield enough DNA for library preparation. If your research facility does not have a cell counter on hand or your concentration is a bit lower, consider sending a larger volume of sample. Let The Sequencing Center know so we can adjust our protocols for maximum DNA extraction efficiency. This is an easy first step to start your project with minimal delays.

DNA Concentration

If you plan to submit extracted DNA, start by referring to our sample submission guidelines for required concentration values. During library preparation, the DNA will go through enzymatic shearing and replication phases, so higher DNA concentrations ensures that your sample will maintain enough integrity. Samples on the threshold of the minimum concentration risk becoming too fragmented and may fail to pass quality control points later on in library prep. These late stage failures can delay a project and may require a complete re-submission of the sample.

Many labs use spectrophotometers for DNA concentration checks, but we recommend using a fluorometer whenever possible. Fluorometers specifically quantify only double-stranded DNA, whereas spectrophotometers are known to also register RNA, proteins, and other contaminants that can skew the concentration value. Having an accurate concentration value increases the likelihood that your sample will pass all downstream quality control checks.

Organization = Expedition

You just finished preparing your high quality samples. Now what? Let’s organize your samples so they’re easy to read and process quickly when they arrive at The Sequencing Center.

Label Samples Clearly

This can’t be stressed enough. Whenever possible, try to use a digital sticker printer to label your samples. This reduces legibility confusion often seen with handwritten labeling. If you have to handwrite the sample names on the tube, opt for writing on laboratory tape instead of directly on the tube. This reduces potential smearing that may occur on the tube due to handling or condensation during transportation. Again, if you have to handwrite your samples be mindful of characters that can look similar such as “S” and “5” or “I” and “1”. Do your best to write these characters distinctly to avoid confusion, or find a colleague with clear handwriting who can write on the label for you.

Sample Packing List

At The Sequencing Center, we send a packing list during your onboarding process. This allows us to accurately record the unique sample identifiers and metrics throughout the sequencing process.

It’s best to send both a digital copy to our lab coordinator and include a printed copy in your sample box. This is a time-saving validation step that lets us quickly confirm we have all your samples and that they are labeled identically to what we read on the sample tubes. This also helps us avoid emailing you to verify sample names.

Organize Your Sample Box

Your samples can be delivered in any way that’s convenient, but it saves a lot of time when they’re backed in grid-divided boxes and the tubes are ordered identically to your sample packing list. Any variation of ordered grouping like this significantly expedites the sample check-in process and lets our team continue onto sequencing faster.

Pack to Protect

Alright, you made it to the final step and are ready to send off your samples. How can you ensure they arrive to us safely and without delays?

Wrap in Parafilm

Before anything else, make sure all sample tubes have parafilm securely wrapped around the lids to prevent spilling. Nothing is more devastating than getting an email saying that your samples exploded all over the shipping box during transit.

Keep Your Samples Cool

Ship your samples with frozen gel packs or dry ice to keep the temperature consistent throughout transit. This is especially important for extracted DNA as the fluctuating temperatures of transit can quickly degrade the DNA and ultimately render your samples unusable.

Dry Ice Tip: If you choose to pack with dry ice instead of frozen gel packs, make sure to include the necessary safety and hazard labels stated in the sample submission guidelines. This helps to avoid time-delays or shipment refusals at the post office.

Bolster with Bubble Wrap

Bubble wrap, packing paper, peanuts – use whatever you can find to prevent your samples from moving around in your shipping container. It’s hard to predict what’s going to happen during transit and you’ll want to prevent as much internal movement as possible. It’s better to over-stuff your package with protective padding than risk your samples cracking and spilling during transit, which will require more time and money to send in again.

We hope these tips will help you out the next time you’re ready for sequencing. If you have any questions, our team is always available to help. Contact us at info@thesequencingcenter.com