Competence Hub for “Spatial Transcriptomics”

Competence Hubs bring together several Core Facilities to provide a streamlined service for cutting-edge, multidisciplinary techniques.

The competence hub for Spatial Transcriptomics brings together the Microscopy, Genomics and Bioinformatics Core Facilities to help you with cutting-edge analyses at the single-cell level combined with spatial information. We use the CytAssist Visium from 10x Genomics and can perform whole transcriptomic spatial profiling across an entire tissue section, including for fixed samples. 

• The Microscopy/Histology Core Facility provides you with a full service for spatial transcriptomics sample preparation, from clearing to cutting and transfering to the microscopy slide
• The Genomics Core Facility offers you next-generation sequencing services based on Illumina platforms
• The Bioinformatics Core Facility handles your single-cell data analysis

Our competence hub offers you a full service : simply bring us your sample, and we do the clearing, cutting transferring, library preparation and sequencing. We are happy to discuss your project needs; please send an email to imb-spatial-transcriptomics(at)lists.uni-mainz.de. 

To use our services, please schedule an initial user meeting to discuss the outline and feasibility of your project, biosafety, trainings and our user guidelines. The table below shows our services. New methods may be implemented to accommodate users’ needs for specific projects.

10x Genomics Visium CytAssist for FFPE spatial gene expression

Sequencers 

• Illumina NextSeq 2000

Suitable for large-scale projects like Whole Genome Sequencing (WGS), RNA-seq or single-cell studies. 

• Illumina MiniSeq

Suitable for low-throughput projects such as Amplicon-seq, Targeted-seq, applications for small genome organisms or to benchmark new protocols, with a maximum yield of 7.5 Gb.

Acknowledgements/ Co-authorships

“An acknowledgement of the Core Facilities in your publication is important and more than just a nice way to say thank you. Your acknowledgement matters!”

Acknowledgements are the currency by which Core Facilities are measured: they help us prove our value and our contribution to research results.  Acknowledging Core Facilities shows that we are important partners in the scientific community, and it allows us to maintain funding and make further investment in the Core Facilities. In the case that Core Facility staff members have contributed significantly to your research project, we ask that you treat them the same way you would treat any other collaborator and consider a co-authorship. 

Specific examples of how to properly acknowledge our Core Facilities can be viewed on our Intranet. In accordance with DFG recommendations, we furthermore ask that you acknowledge any instrumentation that is funded through a DFG major instrumentation grant by including the corresponding project number.