Redefining NGS Library Prep for the Real World: Streamlining for Speed and Savings

How NEBNext UltraExpress^® helps address key challenges at a University Core Genomics Center

In today’s rapidly evolving genomics landscape, core facilities and research groups often need to adapt to evolving demands – such as managing high sample volumes or accelerating experiments to generate sequencing data more quickly. Genomics is a field where technological advancements continuously and rapidly reshape the landscape, necessitating faster and better reagents for faster and better libraries. This is the origin story of the NEBNext UltraExpress Library Prep Kits for DNA, FS DNA, and RNA – innovative solutions designed to meet sequencing demands with unparalleled speed, accuracy and efficiency.

These kits offer a fast workflow, single-condition setup for adaptor concentration and PCR cycle number, minimal hands-on time, and reduced consumables usage and costs. NEBNext UltraExpress is truly streamlined for speed.

Challenging to the Core

At the University of Michigan’s Advanced Genomics Core, the sample variety is astounding – from reptile skin from the Museum of Zoology to surgical samples from the University Medical Center. All demand the same attention to detail and high-quality treatment to transform them into genomic insights. Dr. Olivia Koues, Director of the Advanced Genomics Core, is well acquainted with the challenges of building processes to support the diverse needs of genomic research, where adaptability is crucial. “It’s never the same from day to day. It feels like there's always something new coming out, so if you don't like change, it’s a problem in my facility because we are constantly evolving. We’re trying to stay not just cutting edge but a leader in those fields”. Given the variety and volume of samples processed at Dr. Koues’ facility, the streamlined efficiency of the NEBNext UltraExpress kits becomes even more important. Whether in a core laboratory like the Advanced Genomics Core, which serves as a shared technology resource providing guidance, expertise and services across the organization, or in individual research labs seeking to optimize their sequencing workflows, the adaptability of the NEBNext UltraExpress kits is invaluable. Dr. Koues explains, “We're a large facility, and the samples we receive run the gamut of all the research done at the University of Michigan, which is a large institution. Everything from bulk RNA and DNA to single-cell and spatial tissue blocks and cell suspensions.”

The Need for Speed

Time is critical in any laboratory experiment, and in the Koues lab, the number and variety of samples must be quickly and meticulously prepared before sequencing. The NEBNext UltraExpress library prep kits address this challenge head-on with their short workflow times. For example, the NEBNext UltraExpress RNA library prep workflow has transformed what was once a multi-day process into a single-day protocol. This significantly enhances lab productivity, allowing more samples to be processed and sequenced in a shorter timeframe.

The workflow times for each of the NEBNext UltraExpress kits are as follows:

• NEBNext UltraExpress DNA Library Prep Kit: 1.8 hours

• NEBNext UltraExpress FS DNA Library Prep Kit: 1.75 hours

• NEBNext UltraExpress RNA Library Prep Kit: 3 hours

For Dr. Koues, the flexibility and speed of NEBNext UltraExpress initially caught her attention. “When we consider new kits and methods that we're going to adopt, we try to pick and choose based on what we think can accommodate the most samples. We're constantly trying to streamline and make things efficient because we try to get people the best data possible as quickly as possible.” The projects submitted to the sequencing core may be large or small, but resources are always in demand, and every project is important. Setting expectations for data delivery across the range of projects can be challenging, but the scientists relying on the data have no time to waste.

“The time and robustness of the kit are key because we only have a couple of technicians. Those technicians are prepping all our libraries, not just the bulk RNA or the bulk DNA projects, but they're doing the single-cell library preps, the spatial library preps — anything that feeds onto a sequencer goes through the hands of these two individuals”. Continues Dr. Koues, “Larger projects that come in can be a challenge too. Shorter workflows mean we can prep more samples and turn them around quickly. As the sequencing platforms increase in throughput, we can sequence more samples at once, and we're able to keep that four-week turnaround time for almost all projects.” By combining rapid turnaround and reliable performance, NEBNext UltraExpress helps the University of Michigan Advanced Genomics Core to consistently meet tight deadlines while delivering excellent data quality.

A Single-Condition Workflow

Speed alone speaks to both research and core labs engaged in high-throughput NGS, but simplicity is another feature most users can appreciate. One of the stand-out features of the NEBNext UltraExpress kits is the single-condition workflow which provides a universal protocol that works across a wide range of input masses, sample types, and downstream applications. By removing the requirement for individually adjusted adaptor concentrations and fine-tuned PCR cycle numbers, NEBNext UltraExpress works for most samples within the kit’s stated input range:

• NEBNext UltraExpress DNA Library Prep Kit: 10 – 200 ng pre-sheared DNA

• NEBNext UltraExpress FS DNA Library Prep Kit: 10 – 200 ng intact DNA

• NEBNext UltraExpress RNA Library Prep Kit: 25 – 250 ng total RNA

NEBNext UltraExpress RNA Library Prep (NEB #E3330)

NEBNext UltraExpress DNA Library Prep (NEB #E3325)

NEBNext UltraExpress FS DNA Library Prep (NEB #E3340)

Performance Without Compromise

While the speed and flexibility were initial draws for Dr. Koues to test the NEBNext UltraExpress Kits, the consistent data quality ultimately made the difference, especially for challenging sample types that can sometimes require extensive work due to suboptimal performance.

This is a significant challenge at the University of Michigan Advanced Genomics Core, which accepts samples derived from a broad spectrum of RNA extraction methods, resulting in potentially inconsistent RNA quality. “We don't control how extractions are performed externally, and not all samples come to us DNase-treated or of high quality... I can't control those metrics. Kits that handle contaminants are very important to us, as well as those that can accommodate a range of inputs,” explains Dr. Koues. The Core often deals with what are termed 'fringe' or 'marginal' samples — those samples that others might reject based on not meeting acceptable input amounts and sample quality. It is here that the NEBNext UltraExpress kits have truly made a difference, enhancing outcomes for challenging samples.

It's really helped what we would consider lower input, low-quality samples that have been challenging. We've found that the kits are performing better than anything we've tried in the past, minimizing cleanups, re-preps, or random failures.

Using Fewer Consumables

In addition to the technical advantages of the NEBNext UltraExpress kits, there is a significant reduction in plastic usage, benefiting a lab’s bottom line and its ecological impact. These kits reduce the overall number of tips and tubes by streamlining the workflow and minimizing the number of components required. Whether you’re motivated by the cost savings of needing to purchase fewer tips and tubes, or you’re inspired by a more ecologically friendly library prep kit, NEBNext UltraExpress saves.

Happy Customers, Happy Lab

Implementing the NEBNext UltraExpress Kits marked a significant improvement at the University of Michigan Advanced Genomics Core. Dr. Koues reflects on the transition: “I think there was a lot of buy-in once they ran it and we didn't have some of the issues that we've been having in the past with fall-out samples or excess adaptor dimer — I can't stress that enough, that's the bane of my lab…when you do 96 samples or more, and then QC results come back and a third of them look like junk. Then we have to clean them up, or maybe we have to fail them or re-prep them. That makes work challenging because you're a little disheartened at the end of that process, especially if it happens over and over again.”

Keeping both the scientific community of the University of Michigan and the 28 core lab staff members satisfied and motivated is a priority for Dr. Koues. The UltraExpress Kits are playing an important role. “The staff are really happy with it right now and I'm not the one doing the hands-on work. I'm glad that I'm not getting a lot of complaints. People don't like change, but we've been running this since it launched. We made the switch pretty quickly because it fixed a lot of our issues.”

NEBNext UltraExpress library prep kits for DNA, FS DNA, and RNA represent a leap forward in speed and efficiency. As genomics continues to evolve towards faster sequencing and data interpretation, and researchers ask more questions about the genomic under-pinnings of health and disease in a range of organisms, NEB and the NEBNext UltraExpress kits ensure they have the support they need to answer them faster and with lower resource expenditure than ever before.