(Q38263227)

1 September 2017

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title

Decoding neural transcriptomes and epigenomes via high-throughput sequencing (English)

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high-throughput sequencing

1 September 2017

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2

Guo-li Ming

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author name string

Jaehoon Shin

series ordinal

1

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PubMed ID

25349913

1 September 2017

Hongjun Song

series ordinal

3

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PubMed ID

25349913

1 September 2017

language of work or name

English

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publication date

28 October 2014

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1 September 2017

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1 September 2017

17

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1 September 2017

11

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1 September 2017

1463-1475

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https://scigraph.springernature.com/pub.10.1038/nn.3814

1 September 2017

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Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II

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Neuronal activity modifies the DNA methylation landscape in the adult brain

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Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis

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Cortical DNA methylation maintains remote memory

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Covalent modification of DNA regulates memory formation

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Effect of chronic heroin and cocaine administration on global DNA methylation in brain and liver.

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Epigenetic mechanisms of depression and antidepressant action

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DNA methylation patterns and epigenetic memory

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Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain

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Global epigenomic reconfiguration during mammalian brain development

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Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

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Identification of piRNAs in the central nervous system.

21 January 2018

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A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing

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MicroRNAs regulate brain morphogenesis in zebrafish

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Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training

21 January 2018

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A SUGGESTIVE RELATIONSHIP OF NERVE CELL RNA WITH SPECIFIC SYNAPTIC SITES

21 January 2018

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Distinct DNA methylation patterns of cognitive impairment and trisomy 21 in Down syndrome

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Human-specific histone methylation signatures at transcription start sites in prefrontal neurons

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Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

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Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.

21 January 2018

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A simple method for gene expression and chromatin profiling of individual cell types within a tissue

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Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling.

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Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

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Application of a translational profiling approach for the comparative analysis of CNS cell types

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A translational profiling approach for the molecular characterization of CNS cell types

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

21 January 2018

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RNA-sequencing from single nuclei

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

21 January 2018

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

21 January 2018

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Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

21 January 2018

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Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

21 January 2018

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System wide analyses have underestimated protein abundances and the importance of transcription in mammals

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The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

21 January 2018

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Specific expression of long noncoding RNAs in the mouse brain

21 January 2018

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RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

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Landscape of transcription in human cells

21 January 2018

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Natural RNA circles function as efficient microRNA sponges

21 January 2018

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Antisense transcription in the mammalian transcriptome

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Bidirectional transcription directs both transcriptional gene activation and suppression in human cells

21 January 2018

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Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation.

21 January 2018

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The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 January 2018

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Comprehensive comparative analysis of strand-specific RNA sequencing methods

21 January 2018

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Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

21 January 2018

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Nascent transcript sequencing visualizes transcription at nucleotide resolution

21 January 2018

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Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

21 January 2018

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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

21 January 2018

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Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

21 January 2018

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A unifying hypothesis on mammalian neural stem cell properties in the adult hippocampus

21 January 2018

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Crystal structure of the nucleosome core particle at 2.8 A resolution

21 January 2018

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Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

21 January 2018

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Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain

21 January 2018

1 reference

Translating the Histone Code

21 January 2018

1 reference

Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III

21 January 2018

1 reference

Histone recognition and large-scale structural analysis of the human bromodomain family

21 January 2018

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Recovery of learning and memory is associated with chromatin remodelling

21 January 2018

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HDAC2 negatively regulates memory formation and synaptic plasticity.

21 January 2018

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Mapping and analysis of chromatin state dynamics in nine human cell types

21 January 2018

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An integrated encyclopedia of DNA elements in the human genome

21 January 2018

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Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

21 January 2018

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Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

21 January 2018

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The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

21 January 2018

1 reference

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

21 January 2018

1 reference

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

21 January 2018

1 reference

Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain

21 January 2018

1 reference

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA.

21 January 2018

1 reference

Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites

21 January 2018

1 reference

Genome-wide evolutionary analysis of eukaryotic DNA methylation.

21 January 2018

1 reference

DNA methylation supports intrinsic epigenetic memory in mammalian cells

21 January 2018

1 reference

DNA methylation does not stably lock gene expression but instead serves as a molecular mark for gene silencing memory

21 January 2018

1 reference

Chromatin structure is required to block transcription of the methylated herpes simplex virus thymidine kinase gene

21 January 2018

1 reference

Genomic DNA methylation: the mark and its mediators

21 January 2018

1 reference

Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex

21 January 2018

1 reference

Human DNA methylomes at base resolution show widespread epigenomic differences

21 January 2018

1 reference

Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes

21 January 2018

1 reference

Conserved role of intragenic DNA methylation in regulating alternative promoters

21 January 2018

1 reference

Epigenetic choreographers of neurogenesis in the adult mammalian brain

21 January 2018

1 reference

Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.

21 January 2018

1 reference

Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens

21 January 2018

1 reference

DNA methylation regulates cocaine-induced behavioral sensitization in mice

21 January 2018

1 reference

Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory

21 January 2018

1 reference

DNA methylation and memory formation

21 January 2018

1 reference

Reaction of sodium bisulfite with uracil, cytosine, and their derivatives

21 January 2018

1 reference

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands

21 January 2018

1 reference

The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing

21 January 2018

1 reference

Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming

21 January 2018

1 reference

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.

21 January 2018

1 reference

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.

21 January 2018

1 reference

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

21 January 2018

1 reference

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

21 January 2018

1 reference

Cytosine methylation and CpG, TpG (CpA) and TpA frequencies

21 January 2018

1 reference

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

21 January 2018

1 reference

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

21 January 2018

1 reference

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

21 January 2018

1 reference

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

21 January 2018

1 reference

Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.

21 January 2018

1 reference

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

21 January 2018

1 reference

Analysis of chromatin structure by in vivo formaldehyde cross-linking.

21 January 2018

1 reference

Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene

21 January 2018

1 reference

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

21 January 2018

1 reference

High-resolution profiling of histone methylations in the human genome

21 January 2018

1 reference

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

1 reference

Surveying the epigenomic landscape, one base at a time

21 January 2018

1 reference

High-resolution mapping of transcription factor binding sites on native chromatin

21 January 2018

1 reference

Micrococcal nuclease does not substantially bias nucleosome mapping

21 January 2018

1 reference

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

21 January 2018

1 reference

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

21 January 2018

1 reference

Chromosomal subunits in active genes have an altered conformation

21 January 2018

1 reference

Sequence and chromatin determinants of cell-type-specific transcription factor binding

21 January 2018

1 reference

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

21 January 2018

1 reference

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

21 January 2018

1 reference

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

21 January 2018

1 reference

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

21 January 2018

1 reference

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

21 January 2018

1 reference

Interchromosomal associations between alternatively expressed loci

21 January 2018

1 reference

The accessible chromatin landscape of the human genome

21 January 2018

1 reference

Capturing chromosome conformation

21 January 2018

1 reference

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).

21 January 2018

1 reference

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

21 January 2018

1 reference

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

21 January 2018

1 reference

A global map of p53 transcription-factor binding sites in the human genome

21 January 2018

1 reference

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

21 January 2018

1 reference

Asymmetrically modified nucleosomes

21 January 2018

1 reference

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

21 January 2018

1 reference

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

21 January 2018

1 reference

Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication

21 January 2018

1 reference

Comprehensive human genome amplification using multiple displacement amplification

21 January 2018

1 reference

mRNA-Seq whole-transcriptome analysis of a single cell

21 January 2018

1 reference

Highly multiplexed subcellular RNA sequencing in situ

21 January 2018

1 reference

Accurate whole human genome sequencing using reversible terminator chemistry

21 January 2018

1 reference

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies.

21 January 2018

1 reference

Performance comparison of benchtop high-throughput sequencing platforms

21 January 2018

1 reference

Real-time DNA sequencing from single polymerase molecules

21 January 2018

1 reference

The potential and challenges of nanopore sequencing

21 January 2018

1 reference

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

21 January 2018

1 reference

Analytical tools and current challenges in the modern era of neuroepigenomics

21 January 2018

1 reference

PubMed Central

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6195198

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

5 November 2018

1 reference

PubMed Central

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6195198

DNA-binding factors shape the mouse methylome at distal regulatory regions

5 November 2018

1 reference

PubMed Central

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6195198

Pervasive combinatorial modification of histone H3 in human cells

5 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25349913

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Modulation of chromatin folding by histone acetylation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25349913

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NN.3814

1 reference

1 September 2017

0 references

1 reference

PubMed ID

25349913