Single-cell sequencing techniques from individual to multiomics analyses

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

(2019) Tsukasa Kouno et al.   Nature Communications

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

(2019) Longqi Liu et al.   Nature Communications

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

(2019) Wai Lim Ku et al.   NATURE METHODS

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

(2019) Craig L. Bohrson et al.   NATURE GENETICS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

(2019) Lei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clonal selection with Ras pathway activation mediates secondary clinical resistance to selective FLT3 inhibition in acute myeloid leukemia

(2019) Christine M. McMahon et al.   Cancer Discovery

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

(2019) Koos Rooijers et al.   NATURE BIOTECHNOLOGY

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Genome aging: somatic mutation in the brain links age-related decline with disease and nominates pathogenic mechanisms

(2019) Michael A Lodato et al.   HUMAN MOLECULAR GENETICS

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

(2019) Chenxu Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

(2018) Anna K. Casasent et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response

(2018) Yukie Kashima et al.   Scientific Reports

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

(2017) Xiao Dong et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Aging and neurodegeneration are associated with increased mutations in single human neurons

(2017) Michael A. Lodato et al.   SCIENCE

Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis

(2017) Taejeong Bae et al.   SCIENCE

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

(2016) David A. duVerle et al.   BMC BIOINFORMATICS

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

(2016) Ruli Gao et al.   NATURE GENETICS

Monovar: single-nucleotide variant detection in single cells

(2016) Hamim Zafar et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

A highly sensitive and accurate gene expression analysis by sequencing (“bead-seq”) for a single cell

(2015) Hiroko Matsunaga et al.   ANALYTICAL BIOCHEMISTRY

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment

(2015) Ayako Suzuki et al.   GENOME BIOLOGY

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE