Spatial Genomics Now Available for Everyone at the DRESDEN-concept Genome Center

The DRESDEN-concept Genome Center (DcGC) now offers spatial genomics, a paradigm shift in gene expression analysis. Two new workflows allow the researchers to study high-throughput gene expression directly in the tissue and get information on cell organization in space, cell states, and the interaction between the cells. Contact the DcGC team and discuss how to implement spatial genomics in your projects and grant applications.

In collaboration with the Histology Facility and Light Microscopy Facility at the Center for Molecular and Cellular Bioengineering (CMCB), the DcGC experts in Spatial and Bioinformatics teams have streamlined multiple workflows from sample preparation to data analysis.

The teams have already generated high-quality datasets and are working on process optimization and improvement of resolution. At the moment, the team offers two separate workflows Visium and Xenium, depending on whether the readout is based on the sequencing or imaging data. In-depth information about both workflows is available below.

Everyone interested in spatial omics, no matter if at the brainstorming, experimental, or grant application stage, is welcome to contact the DcGC team and discuss ideas and get support. The DFG also offers new funding opportunities for sequencing costs that can be used for such projects. Read more here.

Contact:

DRESDEN-concept Genome Center
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The Spatial Genomics Workflows:

Visium

Sequencing-based workflow for unbiased, full transcriptome studies. This system is based on spatially indexed slides, containing spatial barcoded primers in two different resolutions: (A) 55 µm diameter spots or (B) 2x2 µm barcoded squares (2x2 µm version only for mouse and human at the moment)

Tissue sections are placed on the slides and permeabilized so that the mRNA is captured by the primers. After reverse transcription, the resulting cDNA contains the spatial barcode that allows to track back the original location of each mRNA molecule.

The Visium workflow can be applied to fresh frozen, fixed frozen, FFPE and archived sections.

In the case of human FFPE samples, it is possible to simultaneously detect immune proteins with a Human Immune Cell Profiling Panel composed of 35 antibodies.

Xenium

Imaging-based high-throughput in-situ technology, enabling targeted mapping of hundreds of RNA molecules, including isoforms and gene fusions, at subcellular resolution. This system is based on gene-specific barcoded padlockprobes that hybridize to the RNAs of interest, followed by internal ligation and rolling circle amplification. The amplified gene-specific barcodes are then detected by hybridization of fluorescently labeled probes. Successive rounds of probe hybridization, imaging and probe removal allows for a highly multiplexed assay using a combinatorial coding scheme.

The Xenium workflow can be applied to fresh frozen and FFPE samples, and it is possible to use pre-designed gene panels as well as custom panels with your genes of interest.