Reference

External references

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Asp, M., Bergenstråhle, J., & Lundeberg, J. Spatially resolved transcriptomes—next generation tools for tissue exploration. BioEssays, 42(10) (2020).
Larsson, L., Frisén, J. & Lundeberg, J. Spatially resolved transcriptomics adds a new dimension to genomics. Nat Methods 18, 15–18 (2021).
Liao, J., Lu, X., Shao, X., Zhu, L., & Fan, X. Uncovering an organ’s molecular architecture at single-cell resolution by spatially resolved transcriptomics. Trends in Biotechnology, 39(1), 43-58 (2021).
Method of the Year 2020: spatially resolved transcriptomics. Nat Methods 18, 1 (2021).
Moses, L., Pachter, L. Museum of spatial transcriptomics. Nat Methods 19, 534–546 (2022).
Ståhl, P.L., Salmén, F., Vickovic, S., Lundmark, A., Navarro, J.F., Magnusson, J., Giacomello, S., Asp, M., Westholm, J.O., Huss, M. and Mollbrink, A. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science, 353(6294), 78-82 (2016). Williams, C.G., Lee, H.J., Asatsuma, T. et al. An introduction to spatial transcriptomics for biomedical research. Genome Med 14, 68 (2022).
Yue, L., Liu, F., Hu, J., Yang, P., Wang, Y., Dong, J., Shu, W., Huang, X. and Wang, S. A guidebook of spatial transcriptomic technologies, data resources and analysis approaches. Computational and Structural Biotechnology Journal, 21, 940-955 (2023).

Glossary

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Barcode

A barcode in spatial transcriptomics is an identifier for a spot on a slide. It is a unique sequence that identifies a spot. The term barcode is generic and identifies other entities in different technologies. For example, in single-cell transcriptomics a barcode identifies a single cell, not a spot on a slide.

Feature

In spatial transcriptomics a gene is a feature. The term feature is generic and refers to different things in different technologies.

Fluorescence in situ hybridization (FISH)

An R package from The Carpentries that is the main user interface for The Carpentries Workbench. More information at: https://carpentries.github.io/sandpaper

Fresh-frozen (FF)

An R package from The Carpentries that is the main user interface for The Carpentries Workbench. More information at: https://carpentries.github.io/sandpaper

Fresh-frozen paraffin embedded (FFPE)

An R package from The Carpentries that is the main user interface for The Carpentries Workbench. More information at: https://carpentries.github.io/sandpaper

Gene detection efficiency

An R package from The Carpentries that provides parsing and validation of markdown source materials for The Carpentries Workbench. More information at: https://carpentries.github.io/pegboard

In situ sequencing (ISS)

An R package from The Carpentries that provides the HTML templates, CSS, and JavaScript code for lesson websites generated via The Carpentries Workbench. More information at: https://carpentries.github.io/varnish

Laser capture microdissection (LCM)

An R package from The Carpentries that provides parsing and validation of markdown source materials for The Carpentries Workbench. More information at: https://carpentries.github.io/pegboard

Seurat

An R package from The Carpentries that provides parsing and validation of markdown source materials for The Carpentries Workbench. More information at: https://carpentries.github.io/pegboard

Single-cell RNA sequencing: (scRNA-seq)

An R package from The Carpentries that provides parsing and validation of markdown source materials for The Carpentries Workbench. More information at: https://carpentries.github.io/pegboard

Spatial resolution

An R package from The Carpentries that provides parsing and validation of markdown source materials for The Carpentries Workbench. More information at: https://carpentries.github.io/pegboard

Spatial transcriptomics (ST)

An R package from The Carpentries that provides parsing and validation of markdown source materials for The Carpentries Workbench. More information at: https://carpentries.github.io/pegboard

Transcriptome

The entire collection of mRNA from a single cell