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Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling

https://doi.org/10.1101/525014
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1 of the 92 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-04): 10.7554/elife.12248 (notice 2018-04-12).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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ggplot2: Elegant Graphics for Data Analysis
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Acute Brain Slice Methods for Adult and Aging Animals: Application of Targeted Patch Clamp Analysis and Optogenetics
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Mapping of fluorescent protein-expressing neurons and axon pathways in adult and developing Thy1-eYFP-H transgenic mice
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A High-Resolution Enhancer Atlas of the Developing Telencephalon
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Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
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Ultraconserved Enhancers Are Required for Normal Development
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A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain Cell Type Targeting and Functionality
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Functional Enhancer Elements Drive Subclass-Selective Expression from Mouse to Primate Neocortex
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Single cell transcriptomics in neuroscience: cell classification and beyond
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Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
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Leptin Directly Activates SF1 Neurons in the VMH, and This Action by Leptin Is Required for Normal Body-Weight Homeostasis
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Leptin Action on GABAergic Neurons Prevents Obesity and Reduces Inhibitory Tone to POMC Neurons
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A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex
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Shaping Our Minds: Stem and Progenitor Cell Diversity in the Mammalian Neocortex
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GENSAT BAC Cre-Recombinase Driver Lines to Study the Functional Organization of Cerebral Cortical and Basal Ganglia Circuits
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Transgenic Mice for Intersectional Targeting of Neural Sensors and Effectors with High Specificity and Performance
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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
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Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex
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Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex
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Genetic Dissection of Neural Circuits: A Decade of Progress
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Rationally Designed MicroRNA-Based Genetic Classifiers Target Specific Neurons in the Brain
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Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
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A mesoscale connectome of the mouse brain
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A comparative encyclopedia of DNA elements in the mouse genome
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Single-cell chromatin accessibility reveals principles of regulatory variation
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The cis-regulatory dynamics of embryonic development at single-cell resolution
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Massively multiplex single-cell Hi-C
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A robust and high-throughput Cre reporting and characterization system for the whole mouse brain
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Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
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Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems
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Neuronal cell-type classification: challenges, opportunities and the path forward
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Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity
inferredcites →https://doi.org/10.1038/s41467-020-14952-3openalex-snapshot
Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons
inferredcites →https://doi.org/10.1038/s41576-018-0089-8openalex-snapshot
Chromatin accessibility and the regulatory epigenome
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Towards a comprehensive catalogue of validated and target-linked human enhancers
inferredcites →https://doi.org/10.1038/s41586-018-0642-9openalex-snapshot
Distinct descending motor cortex pathways and their roles in movement
inferredcites →https://doi.org/10.1038/s41586-018-0654-5openalex-snapshot
Shared and distinct transcriptomic cell types across neocortical areas
inferredcites →https://doi.org/10.1038/s41586-019-1716-zopenalex-snapshot
Hierarchical organization of cortical and thalamic connectivity
inferredcites →https://doi.org/10.1038/s41587-019-0290-0openalex-snapshot
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell
inferredcites →https://doi.org/10.1038/s41592-019-0404-0openalex-snapshot
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues
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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
inferredcites →https://doi.org/10.1038/s41593-019-0431-2openalex-snapshot
Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans
inferredcites →https://doi.org/10.1038/s41593-020-0692-9openalex-snapshot
Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans
inferredcites →https://doi.org/10.1038/s41598-016-0001-8openalex-snapshot
Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease
inferredcites →https://doi.org/10.1038/s41598-018-26803-9openalex-snapshot
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inferredcites →https://doi.org/10.1038/sj.mt.6300027openalex-snapshot
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Cre recombinase-mediated restoration of nigrostriatal dopamine in dopamine-deficient mice reverses hypophagia and bradykinesia
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Developmental and adult phenotyping directly from mutant embryonic stem cells
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Tools for neuroanatomy and neurogenetics in Drosophila
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rtracklayer: an R package for interfacing with genome browsers
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The Sequence Alignment/Map format and SAMtools
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STAR: ultrafast universal RNA-seq aligner
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Correlated Gene Expression and Target Specificity Demonstrate Excitatory Projection Neuron Diversity
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DICE, an efficient system for iterative genomic editing in human pluripotent stem cells
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limma powers differential expression analyses for RNA-sequencing and microarray studies
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Cis-regulatory landscapes of four cell types of the retina
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Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data
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The regulation of myogenin gene expression during the embryonic development of the mouse.
inferredcites →https://doi.org/10.1101/gr.193789.115openalex-snapshot
Massively parallel cis-regulatory analysis in the mammalian central nervous system
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1126/science.1227622openalex-snapshot
The Spatial and Temporal Origin of Chandelier Cells in Mouse Neocortex
inferredcites →https://doi.org/10.1126/science.1232542openalex-snapshot
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
inferredcites →https://doi.org/10.1126/science.aab1687openalex-snapshot
Single-cell–initiated monosynaptic tracing reveals layer-specific cortical network modules
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Joint profiling of chromatin accessibility and gene expression in thousands of single cells
inferredcites →https://doi.org/10.1128/jvi.00254-08openalex-snapshot
In Vitro and In Vivo Gene Therapy Vector Evolution via Multispecies Interbreeding and Retargeting of Adeno-Associated Viruses
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
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Taxa: An R package implementing data standards and methods for taxonomic data
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A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling
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Software for Computing and Annotating Genomic Ranges
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An Inducible and Reversible Mouse Genetic Rescue System
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WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans
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Genetic Labeling of Neuronal Subsets through Enhancer Trapping in Mice
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Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences
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Targeting Cre Recombinase to Specific Neuron Populations with Bacterial Artificial Chromosome Constructs
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Projection-Specific Neuromodulation of Medial Prefrontal Cortex Neurons
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Refinement of Tools for Targeted Gene Expression in Drosophila
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Reshaping Data with the reshape Package
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plater: Read, Tidy, and Display Data from Microtiter Plates
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CellProfiler™: Free, Versatile Software for Automated Biological Image Analysis
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ggbeeswarm: Categorical Scatter (Violin Point) Plots
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Matrix: Sparse and Dense Matrix Classes and Methods
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Rtsne: T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
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Anatomical characterization of Cre driver mice for neural circuit mapping and manipulation
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A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types
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Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
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Author response: Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Nonhuman Primate Optogenetics: Current Status and Future Prospects
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Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts
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Reverse engineering human brain evolution using organoid models
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Functional Enhancer Elements Drive Subclass-Selective Expression from Mouse to Primate Neocortex
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Linking axon morphology to gene expression: a strategy for neuronal cell-type classification
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Enhancer-Driven Gene Expression (EDGE) Enables the Generation of Viral Vectors Specific to Neuronal Subtypes
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Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain
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Development and Arealization of the Cerebral Cortex
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Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network
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Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes
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Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons
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Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons
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Comprehensive analysis of single cell ATAC-seq data with SnapATAC
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Comparative cellular analysis of motor cortex in human, marmoset and mouse
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AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset
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Chromatin accessibility profiling methods
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Optogenetics for light control of biological systems
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Generation of viral vectors specific to neuronal subtypes of targeted brain regions by Enhancer-Driven Gene Expression (EDGE)
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Targeting Subsets of Mammalian Neurons
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Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain
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AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain
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A scalable platform for the development of cell-type-specific viral drivers
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Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex
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