A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

Patch-seq: Past, Present, and Future

(2021) Marcela Lipovsek et al.   JOURNAL OF NEUROSCIENCE

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

A cell atlas of the chick retina based on single-cell transcriptomics

(2021) Masahito Yamagata et al.   eLife

Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas

(2021) Fuguo Wu et al.   Nature Communications

A Casz1–NuRD complex regulates temporal identity transitions in neural progenitors

(2021) Pierre Mattar et al.   Scientific Reports

Atoh7-independent specification of retinal ganglion cell identity

(2021) Justin Brodie-Kommit et al.   Science Advances

Dynamic Polarization of Rab11a Modulates Crb2a Localization and Impacts Signaling to Regulate Retinal Neurogenesis

(2021) Brian S. Clark et al.   Frontiers in Cell and Developmental Biology

Imaging cell lineage with a synthetic digital recording system

(2021) Ke-Huan K. Chow et al.   SCIENCE

A potential role for somatostatin signaling in regulating retinal neurogenesis

(2021) Kurt Weir et al.   Scientific Reports

Foxn4 is a temporal identity factor conferring mid/late-early retinal competence and involved in retinal synaptogenesis

(2020) Shuting Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development

(2020) Haruka Yamamoto et al.   Cell Reports

Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration

(2020) Luz D. Orozco et al.   Cell Reports

Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures

(2020) Akshayalakshmi Sridhar et al.   Cell Reports

STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina

(2020) Nikolas L. Jorstad et al.   Cell Reports

Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development

(2020) Yufeng Lu et al.   DEVELOPMENTAL CELL

MOUSE RETINAL CELL ATLAS: MOLECULAR IDENTIFICATION OF OVER SIXTY AMACRINE CELL TYPES

(2020) Wenjun Yan et al.   JOURNAL OF NEUROSCIENCE

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence

(2020) Soo Seok Hwang et al.   SCIENCE

OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification

(2020) Miruna Georgiana Ghinia Tegla et al.   eLife

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

(2020) Sarah Bowling et al.   CELL

Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells

(2020) Arnav Moudgil et al.   CELL

Different lineage contexts direct common pro-neural factors to specify distinct retinal cell subtypes

(2020) Mei Wang et al.   JOURNAL OF CELL BIOLOGY

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

(2020) Thomas A. Ray et al.   Nature Communications

Cell Atlas of The Human Fovea and Peripheral Retina

(2020) Wenjun Yan et al.   Scientific Reports

Her9/Hes4 is required for retinal photoreceptor development, maintenance, and survival

(2020) Cagney E. Coomer et al.   Scientific Reports

Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution

(2020) Cameron S. Cowan et al.   CELL

Resolving Neurodevelopmental and Vision Disorders Using Organoid Single-Cell Multi-omics

(2020) Giovanna Brancati et al.   NEURON

Emergence of Neuronal Diversity during Vertebrate Brain Development

(2020) Bushra Raj et al.   NEURON

Gene regulatory networks controlling vertebrate retinal regeneration

(2020) Thanh Hoang et al.   SCIENCE

Human Organoids for the Study of Retinal Development and Disease

(2020) Claire M. Bell et al.   Annual Review of Vision Science

Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior

(2020) Yvonne Kölsch et al.   NEURON

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

(2020) Xin Jin et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

(2019) Yi-Rong Peng et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

(2019) Brian S. Clark et al.   NEURON

Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids

(2019) Sangbae Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species

(2019) Genevieve L. Stein-O’Brien et al.   Cell Systems

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

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing

(2019) A.P. Voigt et al.   EXPERIMENTAL EYE RESEARCH

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

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

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

(2019) Kevin Grosselin et al.   NATURE GENETICS

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

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

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

Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis

(2019) Yuqiong Hu et al.   PLOS BIOLOGY

A single‐cell transcriptome atlas of the adult human retina

(2019) Samuel W Lukowski et al.   EMBO JOURNAL

Nucleome Dynamics during Retinal Development

(2019) Jackie L. Norrie et al.   NEURON

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

(2019) Madhvi Menon et al.   Nature Communications

Molecular signatures of retinal ganglion cells revealed through single cell profiling

(2019) Lauren A. Laboissonniere et al.   Scientific Reports

Highly multiplexed single-cell RNA-seq by DNA oligonucleotide tagging of cellular proteins

(2019) Jase Gehring et al.   NATURE BIOTECHNOLOGY

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

(2019) Nicholas M. Tran et al.   NEURON

Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling

(2019) Qingnan Liang et al.   Nature Communications

C8orf46 homolog encodes a novel protein Vexin that is required for neurogenesis in Xenopus laevis

(2018) Kathryn B. Moore et al.   DEVELOPMENTAL BIOLOGY

The dynamics of native Atoh7 protein expression during mouse retinal histogenesis, revealed with a new antibody

(2018) Joel B. Miesfeld et al.   GENE EXPRESSION PATTERNS

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

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

A Translational Repression Complex in Developing Mammalian Neural Stem Cells that Regulates Neuronal Specification

(2018) Siraj K. Zahr et al.   NEURON

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

(2018) Xiao Wang et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

(2018) Bruce A. Rheaume et al.   Nature Communications

Neuronal Migration and Lamination in the Vertebrate Retina

(2018) Rana Amini et al.   Frontiers in Neuroscience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Tumor suppressors BTG1 and BTG2: Beyond growth control

(2018) Laurensia Yuniati et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Neuronal specification in space and time

(2018) Isabel Holguera et al.   SCIENCE

Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina

(2018) Joseph Collin et al.   STEM CELLS

DNER and NFIA are expressed by developing and mature AII amacrine cells in the mouse retina

(2017) Patrick W. Keeley et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Single cell transcriptome profiling of developing chick retinal cells

(2017) Lauren A. Laboissonniere et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Stimulation of functional neuronal regeneration from Müller glia in adult mice

(2017) Nikolas L. Jorstad et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

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

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Neuronal cell-type classification: challenges, opportunities and the path forward

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis

(2017) Issam Aldiri et al.   NEURON

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Modeling Glaucoma: Retinal Ganglion Cells Generated from Induced Pluripotent Stem Cells of Patients with SIX6 Risk Allele Show Developmental Abnormalities

(2017) Pooja Teotia et al.   STEM CELLS

Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells

(2017) Lauren A. Laboissonniere et al.   Jove-Journal of Visualized Experiments

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

The functional diversity of retinal ganglion cells in the mouse

(2016) Tom Baden et al.   NATURE

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Expression Profiling of Developing Zebrafish Retinal Cells

(2016) Madelyn Mullally et al.   Zebrafish

The Ciliary Margin Zone of the Mammalian Retina Generates Retinal Ganglion Cells

(2016) Florencia Marcucci et al.   Cell Reports

Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish

(2016) Mailin Sotolongo-Lopez et al.   PLoS Genetics

Multiple intrinsic factors act in concert with Lhx2 to direct retinal gliogenesis

(2016) Jimmy de Melo et al.   Scientific Reports

The Types of Retinal Ganglion Cells: Current Status and Implications for Neuronal Classification

(2015) Joshua R. Sanes et al.   Annual Review of Neuroscience

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 chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

A Conserved Regulatory Logic Controls Temporal Identity in Mouse Neural Progenitors

(2015) Pierre Mattar et al.   NEURON

Two transcription factors, Pou4f2 and Isl1, are sufficient to specify the retinal ganglion cell fate

(2015) Fuguo Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

The apelin receptor: physiology, pathology, cell signalling, and ligand modulation of a peptide-activated class A GPCR

(2014) Nigel A. Chapman et al.   Biochemistry and Cell Biology

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

Retinal bipolar cells: elementary building blocks of vision

(2014) Thomas Euler et al.   NATURE REVIEWS NEUROSCIENCE

Intrinsically different retinal progenitor cells produce specific types of progeny

(2014) Connie Cepko   NATURE REVIEWS NEUROSCIENCE

ASCL1 reprograms mouse Muller glia into neurogenic retinal progenitors

(2013) J. Pollak et al.   DEVELOPMENT

Otx2 and Onecut1 Promote the Fates of Cone Photoreceptors and Horizontal Cells and Repress Rod Photoreceptors

(2013) Mark M. Emerson et al.   DEVELOPMENTAL CELL

Analysis of gene expression in wild-type and Notch1 mutant retinal cells by single cell profiling

(2013) Karolina Mizeracka et al.   DEVELOPMENTAL DYNAMICS

Exome sequencing and functional analyses suggest that SIX6 is a gene involved in an altered proliferation–differentiation balance early in life and optic nerve degeneration at old age

(2013) Adriana I. Iglesias et al.   HUMAN MOLECULAR GENETICS

Temporal patterning of Drosophila medulla neuroblasts controls neural fates

(2013) Xin Li et al.   NATURE

Connectomic reconstruction of the inner plexiform layer in the mouse retina

(2013) Moritz Helmstaedter et al.   NATURE

Temporal fate specification and neural progenitor competence during development

(2013) Minoree Kohwi et al.   NATURE REVIEWS NEUROSCIENCE

Conserved microRNA pathway regulates developmental timing of retinal neurogenesis

(2013) A. La Torre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of Llgl1 in retinal neuroepithelia reveals links between apical domain size, Notch activity and neurogenesis

(2012) B. S. Clark et al.   DEVELOPMENT

Math5 defines the ganglion cell competence state in a subpopulation of retinal progenitor cells exiting the cell cycle

(2012) Joseph A. Brzezinski et al.   DEVELOPMENTAL BIOLOGY

Protocadherin-17 function in Zebrafish retinal development

(2012) Yun Chen et al.   Developmental Neurobiology

ATOH7 mutations cause autosomal recessive persistent hyperplasia of the primary vitreous

(2012) Lev Prasov et al.   HUMAN MOLECULAR GENETICS

Numb is Required for the Production of Terminal Asymmetric Cell Divisions in the Developing Mouse Retina

(2012) A. Kechad et al.   JOURNAL OF NEUROSCIENCE

Protocadherin 17 acts as a tumour suppressor inducing tumour cell apoptosis and autophagy, and is frequently methylated in gastric and colorectal cancers

(2012) Xiaotong Hu et al.   JOURNAL OF PATHOLOGY

The Neuronal Organization of the Retina

(2012) Richard H. Masland   NEURON

How Variable Clones Build an Invariant Retina

(2012) Jie He et al.   NEURON

Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates

(2012) B. P. Hafler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direction-selective retinal ganglion cells arise from molecularly specified multipotential progenitors

(2012) I. De la Huerta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ascl1 expression defines a subpopulation of lineage-restricted progenitors in the mammalian retina

(2011) Joseph A. Brzezinski et al.   DEVELOPMENT

Identification of a retina-specific Otx2 enhancer element active in immature developing photoreceptors

(2011) Mark M. Emerson et al.   DEVELOPMENTAL BIOLOGY

Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

Reconstruction of rat retinal progenitor cell lineages in vitro reveals a surprising degree of stochasticity in cell fate decisions

(2010) F. L. A. F. Gomes et al.   DEVELOPMENT

Blimp1 Suppresses Chx10 Expression in Differentiating Retinal Photoreceptor Precursors to Ensure Proper Photoreceptor Development

(2010) K. Katoh et al.   JOURNAL OF NEUROSCIENCE

Ascl1a regulates Müller glia dedifferentiation and retinal regeneration through a Lin-28-dependent, let-7 microRNA signalling pathway

(2010) Rajesh Ramachandran et al.   NATURE CELL BIOLOGY

Computational prediction of neural progenitor cell fates

(2010) Andrew R Cohen et al.   NATURE METHODS

Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina

(2010) Anand Swaroop et al.   NATURE REVIEWS NEUROSCIENCE

MATH5 controls the acquisition of multiple retinal cell fates

(2010) Liang Feng et al.   Molecular Brain

Birthdays of retinal amacrine cell subtypes are systematically related to their molecular identity and soma position

(2009) P. Emanuela Voinescu et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Development and diversification of retinal amacrine interneurons at single cell resolution

(2009) T. J. Cherry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development and neurogenic potential of Müller glial cells in the vertebrate retina

(2009) Ashutosh P. Jadhav et al.   PROGRESS IN RETINAL AND EYE RESEARCH

Identification of molecular markers of bipolar cells in the murine retina

(2008) Douglas S. Kim et al.   JOURNAL OF COMPARATIVE NEUROLOGY

The transcriptome of retinal Müller glial cells

(2008) Karin Roesch et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Ikaros Confers Early Temporal Competence to Mouse Retinal Progenitor Cells

(2008) Jimmy Elliott et al.   NEURON

Individual Retinal Progenitor Cells Display Extensive Heterogeneity of Gene Expression

(2008) Jeffrey M. Trimarchi et al.   PLoS One

Stimulation of neural regeneration in the mouse retina

(2008) M. O. Karl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA