FGCZ Genomics > Services
We also provide surface protein co-detection and cell multiplexing as integral components of our services. For a more thorough understanding, please consult the single-cell preparation guidelines provided through the link at the bottom of this page. Within this guideline, you will also find detailed information on preparing single-cell suspensions from various sources.
Note: The more samples we process, the lower the price becomes, as both the sample processing and sequencing costs decrease. For instance, if you process 4 samples with the 10x 3' Gene Expression kit, the total cost will be 10,585 CHF.
Cost estimates are valid for UZH and ETHZ research groups only and non-EU grants.
Cost estimates are non-binding and subject to change.
1. Full-Service Mode: You provide us with the single-cell/nuclei suspension, and we take care of the entire process, from library preparation and sequencing to basic data analysis.
2. Rental Mode: We will provide training on how to load the 10x chip, allowing you to rent the 10x Chromium system for loading in your own lab with your reagents. Subsequently, you can use our user lab for library preparation, with our assistance, offering you maximum flexibility in your workflow.
1. Quality Control Metrics: These metrics assess the quality of the data and the individual cells. They may include metrics like the number of detected genes per cell, the total number of transcripts per cell, and others.
2. Gene Expression Matrix: This matrix contains information about the expression levels of each gene in each individual cell. Rows represent genes, columns represent cells, and the values in the matrix indicate the gene expression levels.
3. Clustering Results: scRNA-seq data is often used to identify distinct cell populations or clusters. The output will include information on which cells belong to each cluster.
4. Visualization Outputs: Output files for data visualization, such as t-SNE or UMAP plots, can help you visualize the relationships between individual cells in a lower-dimensional space.
For additional analyses, such as customized cell annotation, differential gene expression, gene set enrichment analysis (GSEA), trajectory analysis, and cell velocity analysis, please contact with our bioinformatics team.
Questions? Please email sequencing at fgcz.ethz.ch.
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)
Single-cell RNA-seq with cell surface protein detection
Cell Multiplexing
Single-cell Gene Expression Flex protocol
Single-cell Multiomics Analysis
Aim
Single-cell sequencing is revolutionizing our comprehension of essential biological processes, including development, immunity, and pathology. Contemporary techniques empower us to delineate the gene expression, cell surface proteins, TCR/BCR receptors, and chromatin accessibility profiles of thousands of cells at a remarkable resolution, facilitating comprehensive characterization of diverse cell populations, such as tumors or entire organisms. At FGCZ, we have incorporated various solutions to grant our users access to cutting-edge single-cell RNA multiomics technologies.Platforms and methods
We offer comprehensive support for various 10x Genomics Single-cell Multiomics protocols utilizing the 10x Chromium X system and BD Multiomics protocols employing the BD Rhapsody HT system. Our workflows are adaptable to both fresh and fixed single-cell/nuclei suspensions (incl. snPATHO-Seq), depending on the specific protocol requirements.| Application | Platform | Kits | Cell Status | Cell Number Required | Cell Viability Required |
| Gene Expression | 10x | Standard 3' Gene Expression | Fresh | 50,000 | 90% |
| Gene Expression Flex (Single Probe) | 4% PFA fixed | 1 Million | 80% before fixation | ||
| Gene Expression Flex (Four Probes) | 4% PFA fixed | 1 Million/Sample | 80% before fixation | ||
| BD | Gene Expression | Fresh | 80,000 | 90% | |
| Gene Expression + VDJ | 10x | 5' Gene Expression + VDJ | Fresh | 50,000 | 90% |
| BD | Gene Expression + VDJ | Fresh | 80,000 | 90% | |
We also provide surface protein co-detection and cell multiplexing as integral components of our services. For a more thorough understanding, please consult the single-cell preparation guidelines provided through the link at the bottom of this page. Within this guideline, you will also find detailed information on preparing single-cell suspensions from various sources.
Price
The following outlines the cost for various platforms and kits per sample:| Application | Platform | Kits | Cell Number Recovered | Total Cost (CHF) | |
| Gene Expression | 10x | Standard 3' Gene Expression | 10,000 | 3555 | |
| Gene Expression Flex (Single Probe) | 10,000 | 4427 | |||
| Gene Expression Flex (Four Probes) | 10,000 | 6940 | |||
| BD | Gene Expression | 25,000 | 3710 | ||
| Gene Expression + VDJ | 10x | 5' Gene Expression + VDJ | 10,000 | 4335 | |
| BD | Gene Expression + VDJ | 25,000 | 4940 | ||
Note: The more samples we process, the lower the price becomes, as both the sample processing and sequencing costs decrease. For instance, if you process 4 samples with the 10x 3' Gene Expression kit, the total cost will be 10,585 CHF.
Cost estimates are valid for UZH and ETHZ research groups only and non-EU grants.
Cost estimates are non-binding and subject to change.
Service Mode
There are two ways to collaborate with us:1. Full-Service Mode: You provide us with the single-cell/nuclei suspension, and we take care of the entire process, from library preparation and sequencing to basic data analysis.
2. Rental Mode: We will provide training on how to load the 10x chip, allowing you to rent the 10x Chromium system for loading in your own lab with your reagents. Subsequently, you can use our user lab for library preparation, with our assistance, offering you maximum flexibility in your workflow.
Output
Our basic data analysis includes delivering the following outputs:1. Quality Control Metrics: These metrics assess the quality of the data and the individual cells. They may include metrics like the number of detected genes per cell, the total number of transcripts per cell, and others.
2. Gene Expression Matrix: This matrix contains information about the expression levels of each gene in each individual cell. Rows represent genes, columns represent cells, and the values in the matrix indicate the gene expression levels.
3. Clustering Results: scRNA-seq data is often used to identify distinct cell populations or clusters. The output will include information on which cells belong to each cluster.
4. Visualization Outputs: Output files for data visualization, such as t-SNE or UMAP plots, can help you visualize the relationships between individual cells in a lower-dimensional space.
For additional analyses, such as customized cell annotation, differential gene expression, gene set enrichment analysis (GSEA), trajectory analysis, and cell velocity analysis, please contact with our bioinformatics team.
Ordering
Instructions can be found hereFurther development in the pipeline
Single-cell multiomics technologies are undergoing rapid evolution. Presently, we are evaluating commercialized SPLiT-seq protocol from Parse Biosciences (Evercode), PIP-seq (Particle-templated instant partition sequencing) from Fluent Biosciences, and ICELL8 cx Single-Cell system for high-throughput single-cell total RNA-seq and single-cell DNA-seq. If you are interested in learning more about our latest acquisitions and forthcoming advancements, please get in touch with us for additional information.Questions? Please email sequencing at fgcz.ethz.ch.
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)
Resources
How to prepare single-cell suspension for 10x standard gene expression profilingSingle-cell RNA-seq with cell surface protein detection
Cell Multiplexing
Single-cell Gene Expression Flex protocol