Click on the links for relevant publications, protocols and other resources.
Technologies for chromatin genomics and genome editing we have developed
- DamID and pA-DamID: methods for the mapping of in vivo protein-genome interactions.
- m6A-tracer: a derivative of DamID, to visualize DNA that has contacted a protein of interest in living cells.
- TRIP: a method to measure the impact of chromatin on gene regulation at thousands of genomic locations in parallel.
- DSB-TRIP: a variant of TRIP to test the impact of chromatin context on DNA repair.
- TIDE and TIDER: simple, cheap and quantitative methods to measure genome editing efficiency by CRISPR/Cas9
- SuRE: a massively parallel reporter assay to map and measure the activity of regulatory elements in entire mammalian genomes.
New tools under development
- A tool to separate genomic loci (such as enhancers and promoters) spatially inside the cell nucleus
- A variant of SuRE to test the functionality of thousands of enhancer/promoter pairs
- A screen to find proteins that control gene regulation inside LADs
Plasmids
Most of our important plasmids can be obtained from Addgene. For other plasmids please contact us.
Data & Code
Our datasets and code are available from various repositories:
• 4D Nucleome: DamID-seq and pA-DamID-seq maps of nuclear lamina interactions
• GEO: A variety of whole-genome datasets (DamID, mRNA-seq, TRIP, ...)
• OSF: Various types of data (some unpublished), records of lab notebooks
• Github: Code of various published and unpublished projects
Contact us if you are interested!