OpenST: Affordable and Customizable Whole-Transcriptome Spatial Profiling

The DRESDEN-concept Genome Center (DcGC), in collaboration with the Histology and Light Microscopy Facilities of the CMCB Technology Platform, has established an in-house OpenST workflow for spatial transcriptomics. OpenST is now available at the DcGC for projects requiring flexible experimental design and cost-effective whole-transcriptome spatial profiling.

OpenST uses poly(A)-based capture for unbiased whole-transcriptome profiling without predefined probe panels. Its approximately 0.6 µm oligo-coated capture surface supports high-resolution and high-sensitivity spatial analysis.

As an open-source workflow, OpenST allows customization of capture area dimensions, spatial binning, and sequencing depth. Depending on experimental design and sequencing requirements, experimental costs can be approximately one quarter of those of comparable commercial assays. This flexibility makes OpenST suitable for projects requiring tailored spatial coverage, analysis of multiple tissue sections, or cost-effective 3D transcriptomic reconstruction.

DcGC workflow is based and adapted from 3 publications:

https://www.sciencedirect.com/science/article/pii/S2667237524002042?via%3Dihub

https://www.nature.com/articles/s41596-024-01065-0

https://www.cell.com/cell/fulltext/S0092-8674(24)00636-6#figs2

Interested? Please contact DcGC to discuss OpenST for your project: