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The accessible chromatin landscape of the hippocampus at single-cell resolution

https://doi.org/10.1101/407668
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What this work says

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

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Stereological estimation of the total number of neurons in the murine hippocampus using the optical disector
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Alterations of Glial Cells in the Mouse Hippocampus During Postnatal Development
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The hippocampus as a spatial map. Preliminary evidence from unit activity in the freely-moving rat
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The role of the right hippocampus in the recall of spatial location
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Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation
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Molecular Architecture of the Mouse Nervous System
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A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
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Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain
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Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc
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Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
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High-Throughput Single-Cell Sequencing with Linear Amplification
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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
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Segment-specific expression of a zinc-finger gene in the developing nervous system of the mouse
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Widespread transcription at neuronal activity-regulated enhancers
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Topological domains in mammalian genomes identified by analysis of chromatin interactions
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The accessible chromatin landscape of the human genome
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Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease
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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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Developmental diversification of cortical inhibitory interneurons
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Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
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Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
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Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
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Sequencing thousands of single-cell genomes with combinatorial indexing
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Massively multiplex single-cell Hi-C
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chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
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Massively parallel single-nucleus RNA-seq with DroNc-seq
inferredcites →https://doi.org/10.1038/nn.4170openalex-snapshot
Stimulus-specific combinatorial functionality of neuronal c-fos enhancers
inferredcites →https://doi.org/10.1038/nn.4494openalex-snapshot
Neuronal activity modifies the chromatin accessibility landscape in the adult brain
inferredcites →https://doi.org/10.1038/s41593-018-0079-3openalex-snapshot
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
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The hematopoietic regulator, ELF-1, enhances the transcriptional response to Interferon-β of the OAS1 anti-viral gene
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Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity.
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Predictive modelling of gene expression from transcriptional regulatory elements
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Fast and accurate short read alignment with Burrows–Wheeler transform
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BEDTools: a flexible suite of utilities for comparing genomic features
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inferredcites →https://doi.org/10.1101/gr.178319.114openalex-snapshot
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
inferredcites →https://doi.org/10.1101/gr.190595.115openalex-snapshot
Defining cell types and states with single-cell genomics
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.14400openalex-snapshot
Glutamine Synthetase: Glial Localization in Brain
inferredcites →https://doi.org/10.1126/science.aaa1934openalex-snapshot
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-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.aam8940openalex-snapshot
Comprehensive single-cell transcriptional profiling of a multicellular organism
inferredcites →https://doi.org/10.1136/jnnp.20.1.11openalex-snapshot
LOSS OF RECENT MEMORY AFTER BILATERAL HIPPOCAMPAL LESIONS
inferredcites →https://doi.org/10.1152/jn.1961.24.3.225openalex-snapshot
ELECTROPHYSIOLOGY OF HIPPOCAMPAL NEURONS: I. SEQUENTIAL INVASION AND SYNAPTIC ORGANIZATION
inferredcites →https://doi.org/10.1152/jn.1961.24.3.243openalex-snapshot
ELECTROPHYSIOLOGY OF HIPPOCAMPAL NEURONS: II. AFTER-POTENTIALS AND REPETITIVE FIRING
inferredcites →https://doi.org/10.1152/jn.1961.24.3.260openalex-snapshot
ELECTROPHYSIOLOGY OF HIPPOCAMPAL NEURONS: III. FIRING LEVEL AND TIME CONSTANT
inferredcites →https://doi.org/10.1152/jn.1961.24.3.272openalex-snapshot
ELECTROPHYSIOLOGY OF HIPPOCAMPAL NEURONS: IV. FAST PREPOTENTIALS
inferredcites →https://doi.org/10.1159/000111955openalex-snapshot
Glutamine Synthetase: A Marker of an Astroglial Subpopulation in Primary Cultures of Defined Brain Areas
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s40064-015-1194-1openalex-snapshot
SOX3 expression in the glial system of the developing and adult mouse cerebellum
inferredcites →https://doi.org/10.1242/jcs.01589openalex-snapshot
AP-1 subunits: quarrel and harmony among siblings
inferredcites →https://doi.org/10.1371/journal.pone.0004779openalex-snapshot
Neurogenin2 Directs Granule Neuroblast Production and Amplification while NeuroD1 Specifies Neuronal Fate during Hippocampal Neurogenesis
inferredcites →https://doi.org/10.1523/eneuro.0255-16.2017openalex-snapshot
NEUROD2 RegulatesStim1Expression and Store-Operated Calcium Entry in Cortical Neurons
inferredcites →https://doi.org/10.1523/jneurosci.06-10-02950.1986openalex-snapshot
Human amnesia and the medial temporal region: enduring memory impairment following a bilateral lesion limited to field CA1 of the hippocampus
inferredcites →https://doi.org/10.1523/jneurosci.1860-14.2014openalex-snapshot
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
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Unique Expression Patterns of Cell Fate Molecules Delineate Sequential Stages of Dentate Gyrus Development
inferredcites →https://doi.org/10.1523/jneurosci.2738-17.2018openalex-snapshot
Remote Memory and Cortical Synaptic Plasticity Require Neuronal CCCTC-Binding Factor (CTCF)
inferredcites →https://doi.org/10.1523/jneurosci.4710-03.2004openalex-snapshot
Defining a Molecular Atlas of the Hippocampus Using DNA Microarrays and High-Throughput In Situ Hybridization
inferredcites →https://doi.org/10.1523/jneurosci.6088-10.2011openalex-snapshot
Preemptive Regulation of Intracellular pH in Hippocampal Neurons by a Dual Mechanism of Depolarization-Induced Alkalinization
inferredcites →https://doi.org/10.15252/embj.201490791openalex-snapshot
USP18 lack in microglia causes destructive interferonopathy of the mouse brain
inferredcites →https://doi.org/10.15252/embj.201591206openalex-snapshot
NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program
inferredcites →https://doi.org/10.7554/elife.14997openalex-snapshot
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons

What points at this work

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

inferred← citeshttps://doi.org/10.1101/637256openalex-snapshot
Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis
inferred← citeshttps://doi.org/10.1101/gr.271791.120openalex-snapshot
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
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