Single-cell RNA sequencing for the study of development, physiology and disease

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf

(2018) Bliss Magella et al.   DEVELOPMENTAL BIOLOGY

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut

(2018) Charles A. Herring et al.   Cell Systems

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing

(2017) Qin Tang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Single-cell RNA-sequence analysis of mouse glomerular mesangial cells uncovers mesangial cell essential genes

(2017) Yuqiu Lu et al.   KIDNEY INTERNATIONAL

Genome-wide identification of genes essential for podocyte cytoskeletons based on single-cell RNA sequencing

(2017) Yuqiu Lu et al.   KIDNEY INTERNATIONAL

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq

(2017) Lihe Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development

(2017) Yina Du et al.   THORAX

Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo

(2017) Cindy T.J. van Velthoven et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array

(2017) Hannah Hochgerner et al.   Scientific Reports

SCell: integrated analysis of single-cell RNA-seq data

(2016) Aaron Diaz et al.   BIOINFORMATICS

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Single-Cell Resolution of Temporal Gene Expression during Heart Development

(2016) Daniel M. DeLaughter et al.   DEVELOPMENTAL CELL

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

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

(2016) Itay Tirosh et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

(2016) Suguna Rani Krishnaswami et al.   Nature Protocols

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

(2016) I. Tirosh et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

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

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis

(2015) Minoru Takasato et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Single cell dissection of early kidney development: multilineage priming

(2014) E. W. Brunskill et al.   DEVELOPMENT

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein 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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

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

(2014) D. A. Jaitin et al.   SCIENCE

Redefining the In Vivo Origin of Metanephric Nephron Progenitors Enables Generation of Complex Kidney Structures from Pluripotent Stem Cells

(2013) Atsuhiro Taguchi et al.   Cell Stem Cell

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Vascularized and functional human liver from an iPSC-derived organ bud transplant

(2013) Takanori Takebe et al.   NATURE

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

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

(2013) Simone Picelli et al.   NATURE METHODS

Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment

(2012) Douglas Hanahan et al.   CANCER CELL

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

(2012) Tamar Hashimshony et al.   Cell Reports

Advances in early kidney specification, development and patterning

(2009) G. R. Dressler   DEVELOPMENT

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Renal Aplasia in Humans Is Associated with RET Mutations

(2008) Michael A. Skinner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues

(2008) Dan Frumkin et al.   BMC BIOTECHNOLOGY

Stromal gene expression predicts clinical outcome in breast cancer

(2008) Greg Finak et al.   NATURE MEDICINE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS