The Unmixing Problem: A Guide to Applying Single-Cell RNA Sequencing to Bone

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

(2019) Samuel G. Rodriques et al.   SCIENCE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Growth plate borderline chondrocytes behave as transient mesenchymal precursor cells

(2019) Koji Mizuhashi et al.   JOURNAL OF BONE AND MINERAL RESEARCH

The bone marrow microenvironment at single-cell resolution

(2019) Anastasia N. Tikhonova et al.   NATURE

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

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

(2018) Elham Azizi et al.   CELL

Placing RNA in context and space - methods for spatially resolved transcriptomics

(2018) Carina Strell et al.   FEBS Journal

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

FAM210A is a novel determinant of bone and muscle structure and strength

(2018) Ken-ichiro Tanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

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

(2018) Alexander B. Rosenberg et al.   SCIENCE

An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters

(2018) Neha Bhagwat et al.   Scientific Reports

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

(2018) Luke Zappia et al.   PLoS Computational Biology

Identification of the Human Skeletal Stem Cell

(2018) Charles K.F. Chan et al.   CELL

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Discovery of a periosteal stem cell mediating intramembranous bone formation

(2018) Shawon Debnath et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems

(2018) Xiannian Zhang et al.   MOLECULAR CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Resting zone of the growth plate houses a unique class of skeletal stem cells

(2018) Koji Mizuhashi et al.   NATURE

Autocrine regulation of mesenchymal progenitor cell fates orchestrates tooth eruption

(2018) Akira Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational approaches for interpreting scRNA-seq data

(2017) Raghd Rostom et al.   FEBS LETTERS

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

(2017) Abbas H Rizvi et al.   NATURE BIOTECHNOLOGY

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

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

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells

(2017) Léo Machado et al.   Cell Reports

Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo

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

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

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

(2016) Dominic Grün et al.   Cell Stem Cell

Targeting of Mesenchymal Stromal Cells byCre-Recombinase Transgenes Commonly Used to Target Osteoblast Lineage Cells

(2016) Jingzhu Zhang et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

BMP signalling in skeletal development, disease and repair

(2016) Valerie S. Salazar et al.   Nature Reviews Endocrinology

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

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

(2016) P. L. Stahl et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

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

(2016) Naomi Habib et al.   SCIENCE

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues

(2016) Idit Kosti et al.   Scientific Reports

Identification and Specification of the Mouse Skeletal Stem Cell

(2015) Charles K.F. Chan et al.   CELL

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

Does FACS perturb gene expression?

(2015) Graham M. Richardson et al.   CYTOMETRY PART A

Bursty Gene Expression in the Intact Mammalian Liver

(2015) Keren Bahar Halpern et al.   MOLECULAR CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Leptin-Receptor-Expressing Mesenchymal Stromal Cells Represent the Main Source of Bone Formed by Adult Bone Marrow

(2014) Bo O. Zhou et al.   Cell Stem Cell

Reproducibility of Results in Preclinical Studies: A Perspective From the Bone Field

(2014) Stavros C Manolagas et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Osteal Tissue Macrophages Are Intercalated throughout Human and Mouse Bone Lining Tissues and Regulate Osteoblast Function In Vitro and In Vivo

(2014) M. K. Chang et al.   JOURNAL OF IMMUNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A subset of chondrogenic cells provides early mesenchymal progenitors in growing bones

(2014) Noriaki Ono et al.   NATURE CELL BIOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Long Bone Structure and Strength Depend on BMP2 from Osteoblasts and Osteocytes, but Not Vascular Endothelial Cells

(2014) Sarah H. McBride et al.   PLoS One

Hypertrophic chondrocytes can become osteoblasts and osteocytes in endochondral bone formation

(2014) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee 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

Chondrocytes Transdifferentiate into Osteoblasts in Endochondral Bone during Development, Postnatal Growth and Fracture Healing in Mice

(2014) Xin Zhou et al.   PLoS Genetics

The effect of cell subset isolation method on gene expression in leukocytes

(2013) Nadejda Beliakova-Bethell et al.   CYTOMETRY PART A

Analysis of αSMA-Labeled Progenitor Cell Commitment Identifies Notch Signaling as an Important Pathway in Fracture Healing

(2013) Brya G Matthews et al.   JOURNAL OF BONE AND MINERAL RESEARCH

RNA-sequencing from single nuclei

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

A Single Recurrent Mutation in the 5′-UTR of IFITM5 Causes Osteogenesis Imperfecta Type V

(2012) Tae-Joon Cho et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Mutation in the 5′-UTR of IFITM5 Creates an In-Frame Start Codon and Causes Autosomal-Dominant Osteogenesis Imperfecta Type V with Hyperplastic Callus

(2012) Oliver Semler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

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

(2012) Tamar Hashimshony et al.   Cell Reports

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

In Vivo Fate Mapping Identifies Mesenchymal Progenitor Cells

(2011) Danka Grcevic et al.   STEM CELLS

The Essential Functions of Adipo-osteogenic Progenitors as the Hematopoietic Stem and Progenitor Cell Niche

(2010) Yoshiki Omatsu et al.   IMMUNITY

BMP2 signaling in bone development and repair

(2009) Vicki Rosen   CYTOKINE & GROWTH FACTOR REVIEWS

Use of an alpha-smooth muscle actin GFP reporter to identify an osteoprogenitor population

(2008) Zana Kalajzic et al.   BONE

Bril: A Novel Bone-Specific Modulator of Mineralization

(2008) Pierre Moffatt et al.   JOURNAL OF BONE AND MINERAL RESEARCH