Competence Hub for “Single-Cell Genomics”
Competence Hubs bring together several Core Facilities to provide a streamlined service for cutting-edge, multidisciplinary techniques.
The competence hub for Single-Cell Genomics brings together the Flow Cytometry, Genomics and Bioinformatics Core Facilities to provide you with a streamlined service for cutting-edge research at the single-cell level. We offer different protocols for single-cell analysis (see below), as well as an extensive portfolio of single-cell NGS approaches, including 10x genomics platforms, Parse Biosciences and Scale Biosciences.
- The Flow Cytometry Core Facility provides you with a full service for sorting single cells for single-cell genomics approaches
- The Genomics Core Facility offers you next-generation sequencing (NGS) services based on Illumina platforms
- The Bioinformatics Core Facility handles your single-cell data analysis
Our competence hub offers you a full service for single-cell genomics: simply bring us your clean cell population, and we do the sorting, library preparation and sequencing. We are happy to discuss your project needs; please send an email to imb-singlecell-genomics(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.
| Applications | Methods | Library prep kits |
|---|---|---|
| Single-cell sequencing | SmartSeq2 scRNA-Seq | Protocol adapted from Picelli et al. Nat. Protoc. 2014 |
| 10x 3' gene expression | Chromium GEM-X Single Cell 3' Kit v4 | |
| 10x 5' GE & CRISPR/V(D)J | Chromium Next GEM Single Cell 5' Kit v3 & 5' CRISPR Kit | |
| 10x scMultiome(ATAC & GE) | Chromium Next GEM Single Cell Multiome ATAC + Gene Expression | |
| 10x Fixed RNA profiling | Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit | |
| Parse Biosciences Evercode | Evercode™ WT Mini kit | |
| Scale Biosciences scRNA-seq | Single Cell RNA Sequencing Kit |
Key instruments
Cell sorter
- BD FACSAria
4 lasers, 16 parameters - Invitrogen Bigfoot
5 lasers, 53 parameters
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
Single-cell technology
- 10X Genomics iX Chromium: Using the iX Chromium and 10x Genomics gel-bead in emulsion (GEM) technology, we offer single-cell or single-nuclei ATAC, RNA or Multiome (ATAC and RNA) sequencing, as well as fixed RNA profiling, allowing sample multiplexing
- We also perform plate-based, single-cell RNA library prep with slit-pool barcoding methods
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.