Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed important advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts
A systematic comparison of 11 sequencing-based spatial transcriptomics methods reveals molecular diffusion as a critical variable that influences the effective resolution and data interpretation across platforms. Our benchmarking study should aid biologists in selecting the most appropriate method for their sp...
36,37]; (3) a probe-based method that counts barcode probes of known targets to obtain spatial information; and (4) image-guided spatially resolved single-cell RNA sequencing; in which individual cells in a region of
The assignment of the spatial distance to plaque per fluorescence punctum is based on the spatial coordinates per punctum provided by CARTANA. The metadata generated by this image analysis was further applied in the data analysis of the in situ sequencing experiment. We used QuPath to overlay the...
Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Cell Res. 2020;30:763–78. Article CAS PubMed PubMed Central Google Scholar Wculek SK, Malanchi I. Neutrophils support lung colonization of metastasis-initiating breast...
The emerging landscape of spatial profiling technologies 2022, Nature Reviews Genetics Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems 2021, Science Non-genetic mechanisms of therapeutic resistance in cancer 2020, Nature Reviews Cancer Hybridization-based in situ se...
Table 2 Primary spatial transcriptomics and spatial multi-omics technologies Full size table Image-based in situ technologies The image-based in situ technologies evolve from in situ hybridization (ISH) and in situ sequencing (ISS). ISH employs labeled probes to hybridize with target sequences in ...
Clinical and translational values of spatial transcriptomics. Signal Transduct Target Ther. 2022;7(1):111. Article CAS PubMed PubMed Central Google Scholar Guo W, Zhou B, Yang Z, Liu X, Huai Q, Guo L, et al. Integrating microarray-based spatial transcriptomics and single-cell RNA-...
et al. Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nat. Biotechnol. 38, 333–342 (2020). Article CAS PubMed Google Scholar Azizi, E. et al. Single-cell map of diverse immune phenotypes in the ...
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