Integration of whole transcriptome spatial profiling with protein markers

N Ben-Chetrit, X Niu, AD Swett, J Sotelo, MS Jiao… - Nature …, 2023 - nature.com
Spatial transcriptomics and proteomics provide complementary information that
independently transformed our understanding of complex biological processes. However …

The expanding vistas of spatial transcriptomics

L Tian, F Chen, EZ Macosko - Nature Biotechnology, 2023 - nature.com
The formation and maintenance of tissue integrity requires complex, coordinated activities
by thousands of genes and their encoded products. Until recently, transcript levels could …

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

B Pardo, A Spangler, LM Weber, SC Page, SC Hicks… - BMC genomics, 2022 - Springer
Background Spatially-resolved transcriptomics has now enabled the quantification of high-
throughput and transcriptome-wide gene expression in intact tissue while also retaining the …

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

SM Zimmerman, R Fropf, BR Kulasekara… - Genome …, 2022 - genome.cshlp.org
Emerging spatial profiling technology has enabled high-plex molecular profiling in biological
tissues, preserving the spatial and morphological context of gene expression. Here, we …

The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

Spatial transcriptomics at subspot resolution with BayesSpace

E Zhao, MR Stone, X Ren, J Guenthoer… - Nature …, 2021 - nature.com
Recent spatial gene expression technologies enable comprehensive measurement of
transcriptomic profiles while retaining spatial context. However, existing analysis methods …

Spatially resolved transcriptomics and beyond

N Crosetto, M Bienko, A Van Oudenaarden - Nature Reviews Genetics, 2015 - nature.com
Considerable progress in sequencing technologies makes it now possible to study the
genomic and transcriptomic landscape of single cells. However, to better understand the …

Advances in spatial transcriptomic data analysis

R Dries, J Chen, N Del Rossi, MM Khan… - Genome …, 2021 - genome.cshlp.org
Spatial transcriptomics is a rapidly growing field that promises to comprehensively
characterize tissue organization and architecture at the single-cell or subcellular resolution …

Giotto: a toolbox for integrative analysis and visualization of spatial expression data

R Dries, Q Zhu, R Dong, CHL Eng, H Li, K Liu, Y Fu… - Genome biology, 2021 - Springer
Spatial transcriptomic and proteomic technologies have provided new opportunities to
investigate cells in their native microenvironment. Here we present Giotto, a comprehensive …

Spatially resolved transcriptomics adds a new dimension to genomics

L Larsson, J Frisén, J Lundeberg - Nature methods, 2021 - nature.com
As single-cell omics continue to advance, the field of spatially resolved transcriptomics has
emerged with a set of experimental and computational methods to map out the positions of …