High-definition spatial transcriptomics for in situ tissue profiling

By S. Vickovic, Gökçen Eraslan, Fredrik Salmén, J. Klughammer, L. Stenbeck, D. Schapiro, Tarmo Äijö, Richard Bonneau, L. Bergenstråhle, J. F. Navarro and 8 more. Nature Methods, 2019

974 citations recorded by the source corpus.

Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-μm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues. A dense, spatially barcoded bead array captures RNA from histological tissue sections for spatially resolved gene expression analysis.

Subfields: Biomedical Engineering, Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46c7c73f86aef037a5a0ab770000c11da9e7b6e5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Biomedical Engineering

In Biophysics

In Molecular Biology

Citations in the corpus

Integrated analysis of multimodal single-cell data (2020, background): “Moreover, pioneering technological advancements now enable the simultaneous profiling of transcriptome alongside either chromatin accessibility [12-14], DNA methylation [15, 16], nucleosome occupancy [17, 18], or spatial location [19, 20].”
Cell2location maps fine-grained cell types in spatial transcriptomics (2022, neutral): “13 and 14 and Methods).”
Cell segmentation in imaging-based spatial transcriptomics (2021, neutral): “These techniques are being gradually augmented by spatially resolved transcriptomics measurements based on in situ sequencing 5,6 , multiplexed single-molecule fluorescent in situ hybridization (smFISH) 7–9 or spatially barcoded hybridization 10,11 .”
The technological landscape and applications of single-cell multi-omics (2023, methodology): “resolution was achieved by using beads with a diameter of 2 μm, which later was reduced even further 120 .”
Methods and applications for single-cell and spatial multi-omics (2023, background): “These approaches allow for transcriptome-wide profiling through capturing of polyadenylated (poly(A)) RNA transcripts released from fixed and permeabilized tissue sections, making use of thousands of arrayed and spatially barcoded oligo-dT spots (for example, Spatial Transcriptomics 170,176 and 10x ”
Museum of spatial transcriptomics (2020, methodology): “Eﬃciency of HDST is 1.3% per bead compared to smFISH.”
Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease. (2020, neutral): “…procedures like single-cell or single-nuclei approaches and maintain spatial information, the lack of single-cell resolution with ST and the low sensitivity of ISS requires further technological improvements (Eng et al., 2019; Rodriques et al., 2019; Vickovic et al., 2019; Stickels et al., 2020).”
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue (2020, methodology): “A similar method, called high-definition spatial transcriptome (HDST), used 2μm beads in a microwell array chip to further reduce the spot size (Vickovic et al., 2019).”