Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

J Liu, V Tran, VNP Vemuri, A Byrne… - Life Science …, 2023 - life-science-alliance.org
Spatial transcriptomics extends single-cell RNA sequencing (scRNA-seq) by providing
spatial context for cell type identification and analysis. Imaging-based spatial technologies …

[HTML][HTML] Recent advances in spatially resolved transcriptomics: challenges and opportunities

J Lee, M Yoo, J Choi - BMB reports, 2022 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) has greatly advanced our understanding of
cellular heterogeneity by profiling individual cell transcriptomes. However, cell dissociation …

STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data

X Li, C Xiao, J Qi, W Xue, X Xu, Z Mu… - Nucleic Acids …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression
heterogeneities in diverse cell types underlying homeostasis, development and pathological …

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

C Xia, J Fan, G Emanuel, J Hao… - Proceedings of the …, 2019 - National Acad Sciences
The expression profiles and spatial distributions of RNAs regulate many cellular functions.
Image-based transcriptomic approaches provide powerful means to measure both …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

T Biancalani, G Scalia, L Buffoni, R Avasthi, Z Lu… - Nature …, 2021 - nature.com
Charting an organs' biological atlas requires us to spatially resolve the entire single-cell
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …

An introduction to spatial transcriptomics for biomedical research

CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …

Spatial reconstruction of single-cell gene expression data

R Satija, JA Farrell, D Gennert, AF Schier… - Nature …, 2015 - nature.com
Spatial localization is a key determinant of cellular fate and behavior, but methods for
spatially resolved, transcriptome-wide gene expression profiling across complex tissues are …

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing

AA Heydari, SS Sindi - BioRxiv, 2022 - biorxiv.org
Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell
RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single …

Spatial charting of single-cell transcriptomes in tissues

R Wei, S He, S Bai, E Sei, M Hu, A Thompson… - Nature …, 2022 - nature.com
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but
cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile …