Spatial transcriptomics using multiplexed deterministic barcoding in tissue
Johannes Wirth1, Nina Huber1, Kelvin Yin1
1Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany.
Nature Communications
|March 19, 2023
Summary
Multiplexed Deterministic Barcoding in Tissue (xDBiT) enables parallel spatial transcriptomics on nine tissue sections. This method enhances gene and read counts, providing detailed molecular insights into tissue architecture.
Area of Science:
- Biomedical Research
- Genomics
- Molecular Biology
Background:
- Spatially resolved transcriptomics is crucial for understanding tissue function.
- Existing methods have limitations in throughput and resolution.
Purpose of the Study:
- To introduce Multiplexed Deterministic Barcoding in Tissue (xDBiT) for high-throughput spatial transcriptomics.
- To enhance data acquisition efficiency and accuracy for tissue analysis.
Main Methods:
- Development of novel microfluidic chips for mRNA spatial encoding.
- Optimization of biochemical protocols to increase read and gene counts.
- Integration of alignment markers for image and data registration.
- Creation of an open-source computational pipeline for data processing.
Main Results:
- Parallel acquisition of spatially resolved transcriptomes from nine tissue sections.
- Achieved 50 µm resolution over a 1.17 cm² tissue area.
- Increased read and gene counts per spot by one order of magnitude.
- Successfully generated 16 datasets from five murine organs (cerebellum, liver, kidney, spleen, heart).
- Enabled in-depth characterization of the murine kidney via factor analysis and deconvolution.
Conclusions:
- xDBiT significantly advances spatial transcriptomics capabilities.
- The technology facilitates comprehensive molecular profiling of complex tissues.
- Open-source tools support broad adoption and further research in spatial biology.
