The Scientific Genomics Platforms are a research-oriented technology department of the Max Delbrück Center for Molecular Medicine of the Helmholtz Association of German Research Centres (Berlin, Germany). The Scientific Genomics Platforms support and perform cutting-edge research in the life sciences. The focus of the department lays on genome research using next generation sequencing and in particular single cell methodologies.
For EASI-Genomics, the Scientific Genomics Platforms focus on single-cell sequencing applications. This task will comprise consultation and on-site training of users in wet-lab procedures and data analyses. Furthermore, this may comprise labor-intensive treatment of biological samples on site, and cell biological preparation of single cells from various samples (e.g. suspension cells, organoids or primary tissues) using the most suitable combination of technologies such as: FACS, single-cell approaches including microfluidics-, microdroplet- or nanowell-based devices. Finally, this will comprise tailored library preparation, sequencing, and primary and secondary data analyses for/with external users.
Technical equipment and infrastructure
The Scientific Genomics Platforms apply mainly Illumina instruments such as NovaSeq 6000, HiSeq 2500/4000 and NextSeq 500 sequencers. Additionally, long-read sequencing systems from Pacific Biosciences and Oxford Nanopore Technologies are being used.
Moreover, a number of methods for single-cell genomics applications have been established, including FACS-seq (BD Aria III, BD Fusion)), microfluidics (Fluidigm C1), Drop-seq (Dolomite), inDrop (1CellBio), Chromium (10X Genomics), and ICELL8 (Takara).
To analyse sequence data the Scientific Genomics Platforms operate in-house facilities extensively making use of the MDC and BIH scientific computing environment, as well as the computational platforms and tools developed within the German Network of Bioinformatics Infrastructure (de.NBI). Pipelines have been established for multiple sequence data analysis applications, in particular for single cell applications.
Furthermore, for targeted validation of sequencing data single cell qPCR (Fluidigm Biomark, Roche LightCycler,) and single cell immunoblotting (Milo) systems, as well as various microscopy devices for (single molecule) fluorescence in situ hybridisation ((sm) FISH) of mRNAs and for immunofluorescence detection of proteins are available. Within EASI-Genomics the Scientific Genomics Platforms represent a flexible unit to grant external users direct access to a research-oriented genomic infrastructure with a focus on cutting-edge single cell applications.
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