Single Cell Sequencing Service

Single cell sequencing is changing our understanding of fundamental biological processes such as development, immunity or pathology. Current methods enable us to define the gene expression profile of thousands of cells with high resolution, allowing in depth characterization of heterogeneous cell populations such as tumours or even whole organisms. At the FGCZ, we have implemented different solutions to provide our users with access to state-​of-the-art scRNA-​seq technologies. They are based in recently developed protocols that are able to capture the picograms of RNA in a cell and subject them to quantitative RNA sequencing. The scRNA-​seq platforms in our portfolio can be divided in two different categories:

Droplet-​based solutions (10X Genomics)

FAQ 10X Genomics

Description: scRNA-​seq is performed in individual droplets within an emulsion. Each droplet is a nano-​reactor that contains only one cell and the reagents to extract and amplify the RNA. Currently, we are using the commercial Drop-​seq platform from 10X Genomics, which allows simultaneous analysis of 500-​10,000 cells per sample, identifying around 1,000-​5,000 different transcripts per cell (50,000-​200,000 reads per cell). This is the recommended approach for the initial characterization of complex cell populations, such as tumour samples, the discovery of new cell types and the identification of new markers to define cell populations.

Access Mode: Walk in access, full service for users with up to 3 runs.
Main application: Characterization of complex cell populations.

General information:
- 1’000-10’000 recovered cells.
- 50’000 reads per cell with 3’-end transcript coverage (98 bp).
- 1’000-4’000 genes per cell detected as expressed.
- Optional: 5’-end transcript coverage with BCR and TCR sequencing; Surface protein identification (CITE-seq); Feature Barcoding cell hashing (TotalSeq B by BioLegend).

Requirements and considerations:
- 25’000 healthy living cells for recovery of 10’000 cells (actual yield does vary).
- Recommended concentration: 1’000 cells/µl in PBS with 0.04% BSA.
- Really sensitive to cell viability and clumps/debris (control before loading).
- First QC step only possible after cDNA synthesis (2’292.99 CHF).
- Guidelines for sample preparation.

- You can bring us the suspension of live cells and we will process the samples for you. Alternatively, you can rent the Chromium and perform everything on your side (with your reagents), or book our User lab space.

Expected costs (around 3’338.36 CHF per sample):
- Single cell suspension preparation (1’000-10’000 cells): 574.42 CHF for 1-8 samples.
- Library preparation: 1’724.85 CHF per sample.
- Sequencing (500 Mio reads, 98 bp, 3’-end): 944.03 CHF; Corresponds to 50’000 reads for 10’000 cells.
- Optional: Higher read coverage up to 500’000 reads per cell.
- Optional: Bioinformatics data analysis, 880 CHF per sample.
- Optional: Basic Cell Ranger output analysis, 110 CHF per sample.
Cost estimates are valid for UZH and ETHZ research groups only and non-EU grants.
Cost estimates are non-binding and subject to change.

Please click here for the sample submission guidelines

In-​plate solutions (Smart-seq2)

Description: Single cells are sorted in 384-​well plates containing lysis buffer and subsequently subjected to individual RNA-​seq analysis. It allows the identification of around 2,000-​7,000 different transcripts per cell with full-​length coverage (250,000-​1,000,000 reads per cells) and it is the ideal solution for in-​depth transcriptomic characterization of relatively homogenous populations or for the analysis of transcriptomic changes during development or in response to different treatments.

Access Mode: Full Service

Main application: Deep single cell transcriptome analysis of homogeneous cell populations.

General information:
- 384 cells per plate.
- 1M reads per cell with full-length transcript coverage.
- 2’000-7’000 genes per cell detected as expressed.

Requirements and considerations:
- Healthy cells sorted individually in 384-well plates containing 0.8 µl of lysis buffer. Cell sorting in 384-well plates is challenging but optimization possible using in-house colorimetric assay.
- First QC step only possible after cDNA synthesis (1’021.63 CHF).

Expected costs (around 6’547.43 CHF per plate):
- cDNA synthesis: 1’021.63 CHF per plate.
- Library preparation: 4’169.71 CHF per plate.
- Sequencing (100 bp, single-end reads): 1’356.10 CHF per plate.
- Option: paired-end reads
- Option: Bioinformatics data analysis, 880 CHF per plate.
Cost estimates are valid for UZH and ETHZ research groups only and non-EU grants.
Cost estimates are non-binding and subject to change.

Please click here for the sample submission guidelines

Ready-made libraries (10X Genomics)

We offer a sequencing only service of ready-made 10X libraries. The minimum is 2 libraries which we will sequence on half of an S1 Flowcell. This will generate around 40K reads for 10K cells. Pricing is around 1099.6 chf per library or 2199.2 chf per lane of an S1. This option gives flexibility to sequence more libraries if you don’t have 10K cells or if you don’t need 40K reads per cell.

Turn around time of 1-2 weeks. If you have more libraries, we we can use full flowcells for better pricing and flexibility.

How to submit samples for Illumina/Short Read Sequencing.pdf

Still have some questions? Please email

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