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 …

Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

HM Bennett, W Stephenson, CM Rose, S Darmanis - Nature Methods, 2023 - nature.com
In the last decade, single-cell RNA sequencing routinely performed on large numbers of
single cells has greatly advanced our understanding of the underlying heterogeneity of …

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

EP Mimitou, CA Lareau, KY Chen… - Nature …, 2021 - nature.com
Recent technological advances have enabled massively parallel chromatin profiling with
scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here …

Single-cell multiomics: technologies and data analysis methods

J Lee, DY Hyeon, D Hwang - Experimental & Molecular Medicine, 2020 - nature.com
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …

Coupled scRNA-seq and intracellular protein activity reveal an immunosuppressive role of TREM2 in cancer

Y Katzenelenbogen, F Sheban, A Yalin, I Yofe… - Cell, 2020 - cell.com
Cell function and activity are regulated through integration of signaling, epigenetic,
transcriptional, and metabolic pathways. Here, we introduce INs-seq, an integrated …

Joint single-cell measurements of nuclear proteins and RNA in vivo

H Chung, CN Parkhurst, EM Magee, D Phillips… - Nature …, 2021 - nature.com
Identifying gene-regulatory targets of nuclear proteins in tissues is a challenge. Here we
describe intranuclear cellular indexing of transcriptomes and epitopes (inCITE-seq), a …

Into the multiverse: advances in single-cell multiomic profiling

S Ogbeide, F Giannese, L Mincarelli, IC Macaulay - Trends in Genetics, 2022 - cell.com
Single-cell transcriptomic approaches have revolutionised the study of complex biological
systems, with the routine measurement of gene expression in thousands of cells enabling …

Time-resolved single-cell RNA-seq using metabolic RNA labelling

F Erhard, AE Saliba, A Lusser, C Toussaint… - Nature Reviews …, 2022 - nature.com
Single-cell RNA genomics technologies are revolutionizing biomedical science by profiling
single cells with unprecedented resolution, providing fundamental insights into the role of …

NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells

AF Chen, B Parks, AS Kathiria, B Ober-Reynolds… - Nature …, 2022 - nature.com
In this work, we describe NEAT-seq (sequencing of nuclear protein epitope abundance,
chromatin accessibility and the transcriptome in single cells), enabling interrogation of …