Abstract
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. However, the integration of robust solutions for the application of these fast-evolving technologies poses a challenge to research core facilities. Moreover, the diversity of research projects and heterogeneity of samples require flexible solutions. In the Functional Genomics Center Zurich (FGCZ), we have implemented different pipelines to provide our users with access to state-of-the-art single cell technologies together with customizable analysis of single cell sequencing data. We are applying our expertise to combine different single-cell sequencing strategies adapting them to the requirements of the research and the complexity of the samples. In the case of scRNA-seq, depending on the expected heterogeneity, an initial characterization using a high throughput methodology, such as 10X Genomics, is our method of choice. This is usually the approach for tumours and clinical samples and it allows us to identify specific markers for the different cell populations. Based on the initial results or if higher resolution is needed, an automated low-volume version of the Smart-seq2 protocol is used to provide in-depth characterization of selected cell populations. The results from both approaches can be combined in our analysis pipeline, allowing us to explore highly heterogeneous samples with low proportion of relevant cells. During the talk, our experience in the implementation of a reliable and flexible single cell sequencing portfolio will be presented, illustrating how we are helping to untangle complex cell populations and to answer challenging biological questions. Moreover, an overview of recent high-throughput technologies, such as SPLIT-seq or micro-well-based solutions, and their use as standardized services offered by core facilities will be discussed.