Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy

Y Liu, Z Xun, K Ma, S Liang, X Li, S Zhou, L Sun… - Journal of …, 2023 - Elsevier
Background & Aims The tumour microenvironment (TME) is a crucial mediator of cancer
progression and therapeutic outcome. The TME subtype correlates with patient response to …

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 …

Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

Spatial profiling technologies illuminate the tumor microenvironment

O Elhanani, R Ben-Uri, L Keren - Cancer cell, 2023 - cell.com
The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

From bulk, single-cell to spatial RNA sequencing

X Li, CY Wang - International journal of oral science, 2021 - nature.com
RNA sequencing (RNAseq) can reveal gene fusions, splicing variants, mutations/indels in
addition to differential gene expression, thus providing a more complete genetic picture than …

Spatially resolved clonal copy number alterations in benign and malignant tissue

A Erickson, M He, E Berglund, M Marklund… - Nature, 2022 - nature.com
Defining the transition from benign to malignant tissue is fundamental to improving early
diagnosis of cancer. Here we use a systematic approach to study spatial genome integrity in …

[HTML][HTML] Microscopic examination of spatial transcriptome using Seq-Scope

CS Cho, J Xi, Y Si, SR Park, JE Hsu, M Kim, G Jun… - Cell, 2021 - cell.com
Spatial barcoding technologies have the potential to reveal histological details of
transcriptomic profiles; however, they are currently limited by their low resolution. Here, we …