Introducing the VIB Single Cell Core
March 24, 2023
This blog post is part of the VIB Technologies campaign.
As VIB’s newest Core Facility, the Single Cell Core culminated from a wide array of single-cell ‘omics’ activities across VIB between 2016 and 2021, after a complex ramp-up. “The single-cell domain is booming,” enthuses Niels Vandamme, Head of the VIB Single Cell Core. “But we can’t investigate single cells without working closely with other adjacent VIB Core Facilities, Tech Watch, and the center-embedded expertise units.”
Single-cell technologies enable life sciences researchers to investigate, down to the molecular level, the most fundamental building blocks of a cell. 2016 marked the moment when several robust single-cell workflows based on commercial applications became available.
“Since then, the use of single-cell omics has been skyrocketing,” asserts Niels Vandamme. “At that time, several labs across VIB were already making use of these workflows. The institute quickly saw the value in integrating VIB’s approach to single cell – but creating a core facility around the technology was no easy job.”
A core isn’t built in a day
Gert Van Isterdael and Stefaan Derveaux, respective Heads of the Flow and Nucleomics Cores, were instrumental in helping Niels set up for success.
Niels: “The Director’s Committee approved the startup of the Single Cell Core in 2020, but for the first six to seven months, Gert, Stefaan, and many experts in the field – including VIB Technologies leaders Saskia Lippens and Geert Van Minnebruggen – contributed their knowledge of what was required and feasible, leading to our first service model.
“At the beginning, I was the only employee of the core and spent many months preparing to run it – its portfolio, modalities, way of working, and how it would be integrated into the institute as a professionalized, embedded technological element.”
“Last year centered around implementing well-functioning, professional workflows based on commercial solutions already running in various settings. This year, we’ll focus on expanding our team, implementing at least two new platforms that were scouted out by Tech Watch, and translating those platforms into a new service portfolio.” - Niels Vandamme, Head of the VIB Single Cell Core
The Single Cell Core was officially launched on 1 January 2022, with recruitment rapidly ramping up across the facility’s sites. “But a core isn’t built in a day – it’s clear that it will take a few years to bring the platform to full maturity,” Niels adds. “Last year centered around implementing well-functioning, professional workflows based on commercial solutions already running in various VIB labs. This year, we’ll focus on expanding our team, implementing at least two new platforms that were scouted out by Tech Watch, and translating those platforms into a new service portfolio.”
The challenges of a dual-site core facility
Transversal integration across core facilities is on the menu for 2023, as the Single Cell Core is co-investing with its partner core facilities in new sequencing platforms and single-cell workflows.
“Many technological advances are made at the interface between technology domains, and because the cores have been working together as one program, we were fully prepared to work as one team across different cores. We don’t work as separate silos.” Niels goes on to say. “This is a logistical shift, but it comes with a cultural shift as well, which has been gradually built up over the past several years. It’s a benefit that the core facility heads have a deep understanding of the needs, activities, and developments happening within our peer cores in order to offer truly integrated services to scientists, institutes, and industry players.”
Integration isn’t a simple task, as the Single Cell, Flow, and Nucleomics Cores are co-located across different campuses in the cities of Ghent and Leuven.
“In terms of financials, management, and logistics, the dual-site setup for the Single Cell Core is fairly complex,” Niels elaborates. “We don’t have separate teams in both cities; rather, one team is working across the two locations. Strategic decisions must be valid across all locations, and it’s crucial for us to make strong connections between them to disseminate information around all the expertise VIB has to offer in terms of single-cell ‘omics’ workflows.”
In Niels’ vision, team members working in the Single Cell Core facility in Ghent, for example, should be able to exit the lab there and, 60 minutes later, ‘turn a corner’ and enter an adjacent lab in Leuven to seamlessly continue their work.
Niels: “Closing these geographical gaps is becoming more and more familiar, as the two facilities are mirrored. Setting up a virtual and physical portal, a gateway between the different locations, has been instrumental. Reagents and personnel are constantly moving back and forth, and these movements are digitally communicated and monitored.”
“The newly established team has been received with open arms on both sites and this dual-site working structure would not have been possible without the help and support of the PIs and the administrative and logistics teams in the hosting centers.” - Niels Vandamme, Head of the VIB Single Cell Core
“The newly established team has been received with open arms on both sites, and this dual-site working structure would not have been possible without the help and support of the PIs and the administrative and logistics teams in the hosting centers.”
Thinking outside the box to move ahead
In ensuring the rich interconnectedness required for this setup to function, Niels, Stefaan, and Gert are setting a prime example.
“As far as I know, we’re the first institute in Europe to really put this to work. Cores used to be set up separately around a specific technology and area of expertise. We’re not just sharing tech and expertise, but plan to share staff between multiple cores.” - Stefaan Derveaux, Head of the VIB Nucleomics Core
“As far as I know, we’re the first institute in Europe to really put this to work. We’re the vanguard here and will serve as the benchmark for this kind of collaboration,” says Stefaan. “Cores used to be set up separately around a specific technology and area of expertise. We’re not just sharing tech and expertise but plan to share staff between multiple cores. In this case, one plus one equals three. I have a strong impression that we’ll be pushed toward this sharing more and more.”
In the field of sequencing/nucleomics, VIB had been fielding questions about its strategy for single cell as early as several years ago. Stefaan: “What I observed here is that the required expertise needs to be very close to the users, which is something we don’t have in nucleomics – our users can be very far away, and that works for us. But with the new model of single cell, it’s necessary to be in proximity to the research teams they are working with – which is what Niels is making happen.”
“This field is developing at a phenomenal pace, and as a result, we are in a unique position to influence decisions related to single-cell workflows and technologies that could have an impact on VIB, and as a result, the broader ecosystem.” - Gert Van Isterdael, Head of the VIB Flow Core
“As the Single Cell Core Facility Head, Niels is on the very cutting edge of single-cell innovation,” adds Gert. “This field is developing at a phenomenal pace, and as a result, we are in a unique position to influence decisions related to single-cell workflows and technologies that could have an impact on VIB and as a result, the broader ecosystem.”
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