FGCZ Genomics > Services
FGCZ – in collaboration with facilities at UZH Irchel, ETH Hoenggerberg and USZ – offers all protocols from the table as a full service.
Please contact sequencing at fgcz.ethz.ch for details about this technology.
Phone: 063 44 6353911 (For pressing issues only please. We prefer if you email us because we are mostly working in the lab so we can't always attend to phone calls)
The number of downstream analyses that become available is constantly expanding and the FGCZ supports all recent approaches.
Spatial Transcriptomics
The Scope
The position and spatial arrangement of cells within a tissue is crucial to our understanding of organ development and pathology. However, the complex organization of tissues has made them difficult to study at a molecular level with sufficient spatial resolution and plexity. While histology and immunohistochemistry methods are fundamental to examining tissue architecture, they do not provide enough information to fully understand changes in gene expression. In order to fill this gap, spatial transcriptomics technologies combine the benefits of traditional image-based protocols with the molecular detail provided by state-of-the art multiomics approaches.The Method
In the Functional Genomics Centre Zurich (FGCZ), we provide support for different 10x Genomics Visium Spatial Gene Expression protocols and Curio Seeker from Curio Bioscience. Depending on the protocol, the workflow is compatible with fresh-frozen, fixed-frozen and FFPE tissue sections and can link high-resolution images of H&E or immunofluorescence stained tissue to spatially distinguishable transcriptome-wide data. Protein co-detection is also possible in a limited scope. This allows to determine where and to which extent different genes are expressed in the tissue.The Workflow
Visium CytAssist and Curio Seeker protocols have different sample requirements. Please consider the following table for further information.| Application | Visium CytAssist | Curio Seeker | ||
| Sample Type | FFPE | Fresh Frozen | Fixed-Frozen | Fresh Frozen |
| Resolution | 55 µm | 10 µm | ||
| Capture Area Size | 6.5 mm or 11 mm | 3 mm or 10 mm | ||
| Scope | Whole transcriptome and limited protein co-detection | Whole transcriptome | ||
| Transcript Detection | Probe-based | poly(A)-capture | ||
| Species | Human or Mouse | Mouse | Any expressing poly(A)-RNA | |
| Required RNA Quality | DV200 ≥ 30% | RIN ≥ 4 | DV200 ≥ 50% | RIN ≥ 7 |
| Sample acceptance at FGCZ | H&E or IF stained and imaged sections on SuperFrost Plus slides | H&E stained and imaged sections on SuperFrost Plus slides | Fresh sections on Curio Seeker Slide (no direct imaging) | |
| Section Thickness | 3 - 10 µm | 10 - 20 µm | 10 - 20 µm | 10 µm |
FGCZ – in collaboration with facilities at UZH Irchel, ETH Hoenggerberg and USZ – offers all protocols from the table as a full service.
Please contact sequencing at fgcz.ethz.ch for details about this technology.
Phone: 063 44 6353911 (For pressing issues only please. We prefer if you email us because we are mostly working in the lab so we can't always attend to phone calls)
The Output
The initial output is a quantification of the spatial expression of different genes in the tissue. This output can be further used to analyse expression clusters, identify cell types and subtypes, assess the heterogeneity of biological samples, identifying markers for given populations, etc.The number of downstream analyses that become available is constantly expanding and the FGCZ supports all recent approaches.