Single‐cell RNA sequencing technologies and applications: A brief overview

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Clonal evolution in liver cancer at single-cell and single-variant resolution

(2021) Xianbin Su et al.   Journal of Hematology & Oncology

Single-Cell Deconvolution of Head and Neck Squamous Cell Carcinoma

(2021) Zongtai Qi et al.   Cancers

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

(2021) Toni M. Delorey et al.   NATURE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Single-cell transcriptome atlas of the leaf and root of rice seedlings

(2021) Yu Wang et al.   Journal of Genetics and Genomics

Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma

(2021) Lichun Ma et al.   JOURNAL OF HEPATOLOGY

Single-cell analysis enters the multiomics age

(2021) Jeffrey M. Perkel   NATURE

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

(2021) Zoe A. Clarke et al.   Nature Protocols

A functional motif of long noncoding RNA Nron against osteoporosis

(2021) Fujun Jin et al.   Nature Communications

Tumor vessel co-option probed by single-cell analysis

(2021) Laure-Anne Teuwen et al.   Cell Reports

deepMNN: Deep Learning-Based Single-Cell RNA Sequencing Data Batch Correction Using Mutual Nearest Neighbors

(2021) Bin Zou et al.   Frontiers in Genetics

An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates

(2020) Jermaine Goveia et al.   CANCER CELL

Single cell RNA-seq reveals the landscape of tumor and infiltrating immune cells in nasopharyngeal cancer

(2020) Jin Zhao et al.   CANCER LETTERS

Single-Cell Transcriptome Atlas of Murine Endothelial Cells

(2020) Joanna Kalucka et al.   CELL

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey

(2020) Nicholas Lytal et al.   Frontiers in Genetics

Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity

(2020) Markus Wolfien et al.   Cells

Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis

(2020) Katerina Rohlenova et al.   Cell Metabolism

Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes

(2020) Joan Camunas-Soler et al.   Cell Metabolism

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq

(2020) Anjun Ma et al.   NUCLEIC ACIDS RESEARCH

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

PscB: A Browser to Explore Plant Single Cell RNA-Sequencing Datasets

(2020) Xiaoli Ma et al.   PLANT PHYSIOLOGY

Gene-edited human stem cell–derived β cells from a patient with monogenic diabetes reverse preexisting diabetes in mice

(2020) Kristina G. Maxwell et al.   Science Translational Medicine

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

(2020) Wei-Ting Chen et al.   CELL

Single-Cell RNA Sequencing of the Cynomolgus Macaque Testis Reveals Conserved Transcriptional Profiles during Mammalian Spermatogenesis

(2020) Xianzhong Lau et al.   DEVELOPMENTAL CELL

Single-cell landscape of immunological responses in patients with COVID-19

(2020) Ji-Yuan Zhang et al.   NATURE IMMUNOLOGY

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

(2020) Hamim Zafar et al.   Nature Communications

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

(2020) Celia Alda-Catalinas et al.   Cell Systems

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

(2020) Andrew L. Ji et al.   CELL

Single-Cell Transcriptome Profiling Reveals β Cell Maturation in Stem Cell-Derived Islets after Transplantation

(2020) Punn Augsornworawat et al.   Cell Reports

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis

(2020) Anna Maria Ranzoni et al.   Cell Stem Cell

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

(2020) Rahul Shaw et al.   Molecular Plant

Multi-modal Single-Cell Analysis Reveals Brain Immune Landscape Plasticity during Aging and Gut Microbiota Dysbiosis

(2020) Samantha M. Golomb et al.   Cell Reports

Single-Nucleus and In Situ RNA–Sequencing Reveal Cell Topographies in the Human Pancreas

(2020) Luca Tosti et al.   GASTROENTEROLOGY

Acquisition of Dynamic Function in Human Stem Cell-Derived β Cells

(2019) Leonardo Velazco-Cruz et al.   Stem Cell Reports

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Cell lineage and communication network inference via optimization for single-cell transcriptomics

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

Charting cellular identity during human in vitro β-cell differentiation

(2019) Adrian Veres et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   SCIENCE

Towards Building a Plant Cell Atlas

(2019) Seung Y. Rhee et al.   TRENDS IN PLANT SCIENCE

Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment

(2019) Anne Dirkse et al.   Nature Communications

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

(2019) Ryan M.J. Genga et al.   Cell Reports

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

(2019) Christine N. Shulse et al.   Cell Reports

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

(2019) Nadav Sharon et al.   Cell Reports

Estimation of immune cell content in tumor using single-cell RNA-seq reference data

(2019) Xiaoqing Yu et al.   BMC CANCER

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

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

(2019) Koos Rooijers et al.   NATURE BIOTECHNOLOGY

scGen predicts single-cell perturbation responses

(2019) Mohammad Lotfollahi et al.   NATURE METHODS

A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys

(2019) Blue B. Lake et al.   Nature Communications

Single-cell reconstruction of follicular remodeling in the human adult ovary

(2019) X. Fan et al.   Nature Communications

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control

(2019) Ivano Legnini et al.   NATURE METHODS

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Single-cell RNA sequencing reveals compartmental remodeling of tumor-infiltrating immune cells induced by anti-CD47 targeting in pancreatic cancer

(2019) Yu Pan et al.   Journal of Hematology & Oncology

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Single-Cell RNA Sequencing Reveals Renal Endothelium Heterogeneity and Metabolic Adaptation to Water Deprivation

(2019) Sébastien J. Dumas et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization

(2019) Chiara Baccin et al.   NATURE CELL BIOLOGY

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Single-cell connectomic analysis of adult mammalian lungs

(2019) Micha Sam Brickman Raredon et al.   Science Advances

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

(2018) Shun H Yip et al.   BRIEFINGS IN BIOINFORMATICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Single-cell RNA sequencing: Technical advancements and biological applications

(2018) Eva Hedlund et al.   MOLECULAR ASPECTS OF MEDICINE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj 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

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

(2018) Luke Zappia et al.   PLoS Computational Biology

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development

(2018) Magdalena K. Sznurkowska et al.   DEVELOPMENTAL CELL

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing

(2018) Michael Bartoschek et al.   Nature Communications

Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes

(2018) Diego Balboa et al.   eLife

Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors

(2018) Nicole A.J. Krentz et al.   Stem Cell Reports

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Effective detection of variation in single-cell transcriptomes using MATQ-seq

(2017) Kuanwei Sheng et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu 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

Single cell transcriptomic profiling of mouse pancreatic progenitors

(2017) Diana E. Stanescu et al.   PHYSIOLOGICAL GENOMICS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

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

(2017) Woosung Chung et al.   Nature Communications

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

A reference human genome dataset of the BGISEQ-500 sequencer

(2017) Jie Huang et al.   GigaScience

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

(2017) Payam Shahi et al.   Scientific Reports

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes

(2016) Yurong Xin et al.   Cell Metabolism

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

(2016) Itay Tirosh et al.   NATURE

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells

(2016) Yurong Xin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) I. Tirosh et al.   SCIENCE

Emergence of Drug Tolerance in Cancer Cell Populations: An Evolutionary Outcome of Selection, Nongenetic Instability, and Stress-Induced Adaptation

(2015) R. H. Chisholm et al.   CANCER RESEARCH

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Controlled induction of human pancreatic progenitors produces functional beta-like cells in vitro

(2015) H. A. Russ et al.   EMBO JOURNAL

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

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

(2014) A. P. Patel et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Regulation of the anti-tumour immune response by cancer-associated fibroblasts

(2014) James Harper et al.   SEMINARS IN CANCER BIOLOGY

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

An estimation of the number of cells in the human body

(2013) Eva Bianconi et al.   ANNALS OF HUMAN BIOLOGY

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Selection and adaptation during metastatic cancer progression

(2013) Christoph A. Klein   NATURE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing

(2013) Chunlei Zhang et al.   PLoS One

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dependency of Colorectal Cancer on a TGF-β-Driven Program in Stromal Cells for Metastasis Initiation

(2012) Alexandre Calon et al.   CANCER CELL

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Transcriptome sequencing of single cells with Smart-Seq

(2012) Jillian J Goetz et al.   NATURE BIOTECHNOLOGY

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

(2012) Tamar Hashimshony et al.   Cell Reports

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor expression in the developing human fetal endocrine pancreas

(2008) B. M. Lyttle et al.   DIABETOLOGIA

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH