Profile six histone PTMs across thousands of single cells in just four days with no specialized setup required. Run eight experiments in parallel and uncover co-localization of histone marks at the same genomic loci. A new standard for scalable, accessible, and multidimensional epigenetic analysis.
Developed by the Jop Kind Group
What is the methodology good for?
This methodology enables high-throughput, single-cell epigenetic profiling of six key histone modifications alongside transcriptomics, without specialized infrastructure. It provides deep insights into the mechanisms governing gene regulation in health and disease and offers a promising approach for more precise and informative tumor classification.
What is/are the main advantages of this methodology over related technologies?
This method enables multiplexed detection of six readouts within the same cell, providing insights into the co-localization of distinct events at identical genomic sites. It supports multiplexed measurements across eight parallel experiments and up to 100,000 cells within a single four-day protocol, which can be performed in any standard research laboratory.
What are the most important limitations of the methodology?
The main limitation of the method is its current cell input requirement. It requires several hundred thousand cells, which restricts its use for epigenetic profiling of samples with limited material, such as small tumor biopsies. We are actively developing a low-input version to overcome this limitation.
What type of samples are compatible with methodology
Cancer cell lines | Primary cells in culture | Organoids | Primary tissue |
Yes | Yes | possibly | possibly |
What future develops to the methodology are you planning, in any?
We are developing protocols to reduce cell input requirements and to make the method compatible with variously preserved patient materials. While the current approach profiles histone modifications, our next goals include extending it to chromatin proteins and transcription factors, as well as increasing multiplexing capacity beyond six profiles per cell.
If someone outside your lab wants to use the methodology, what is the best option?
“We’ve long envisioned a tool that could truly capture the complexity of chromatin states in single cells. Seeing it become accessible to any lab is what drives our work forward.”
Within sCellgen, a spin-off from our group, we are developing commercial kits to make the technology easily accessible to the research community. In parallel, we are creating a computational suite to facilitate and standardize data analysis. For projects not compatible with the standard kit, we can offer on-site training within our group.
The technology can be performed by any skilled molecular biologist in any lab environment.
Name one or more people in your lab that are experienced with the methodology
The people involved within sCellgen are Erica Vos and Esther Uijttewaal. Within the Kind group the most experienced people are Moritz Bauer and Christian Valdes.
Who originally developed the methodology?
The original technology was developed by Silke Lochs and Robin v/d Weide in our group together with coworkers. PMID:38049699. The technology has since improved significantly in specificity, sensitivity and throughput.