Sequencing and Bioinformatics

Project Summary

This service project will provide standardised and advanced workflows for the preparation and analysis of next generation sequencing data of cells derived from the heterocellular heart. This service project will fine-tune methods for isolation and purification of cardiomyocytes and non-myocytes, or their nuclei, from tissue of different species (in collaboration with S2). Standardised protocols will be developed and used for isolation of RNA, chromatin, and DNA from CRC samples, and for preparation of sequencing libraries. In addition, we will provide harmonised data analysis workflows and bioinformatics support for standard RNA-seq, as well as interactive analysis support for specialised protocols. An important aspect will be the development of a CRC-wide resource with easy browser-based access for storage, exchange, visualisation, and mutual mapping of data, using the European Galaxy-Server (in collaboration with INF). This project will develop novel scRNA-seq analysis pipelines, which will be integrated into Galaxy, complementing standard tools (e.g. Scanpy), as well as dedicated developments of individual projects (e.g. RaceID from P01). To allow CRC researchers to use the described methods, S3 will provide regular hands-on workshops for sorting methods, next generation sequencing library generation, and data analysis using the Galaxy platform.