Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity (Q34027627)

30 July 2017

title

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

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22

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26

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Damian Keefe

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Nathan C. Sheffield

Nathan C Sheffield

7

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Alan P. Boyle

Alan P Boyle

4

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Debbie Winter

Deborah Winter

19

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Mikael Huss

Mikael Huss

9

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Darin London

12

Darin London

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24

Gregory E Crawford

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8

Stefan Gräf

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1

Lingyun Song

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25

Jason D Lieb

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23

Vishwanath R Iyer

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30 July 2017

Zhancheng Zhang

2

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Linda L Grasfeder

3

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Paul G Giresi

5

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Bum-Kyu Lee

6

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Zheng Liu

11

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Ryan M McDaniell

13

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Yoichiro Shibata

14

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Kimberly A Showers

15

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Jeremy M Simon

16

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Teresa Vales

17

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Tianyuan Wang

18

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Zhuzhu Zhang

20

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Neil D Clarke

21

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30 July 2017

publication date

12 July 2011

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30 July 2017

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30 July 2017

volume

21

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30 July 2017

issue

10

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30 July 2017

page(s)

1757-1767

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A user's guide to the encyclopedia of DNA elements (ENCODE)

30 July 2017

cites work

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A unique chromatin signature uncovers early developmental enhancers in humans

28 July 2018

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Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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28 July 2018

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Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy

28 July 2018

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Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

28 July 2018

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28 July 2018

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28 July 2018

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Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263

28 July 2018

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Exhaustive search for over-represented DNA sequence motifs with CisFinder

28 July 2018

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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

28 July 2018

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

28 July 2018

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

28 July 2018

1 reference

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UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

28 July 2018

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F-Seq: a feature density estimator for high-throughput sequence tags

28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

High-resolution mapping and characterization of open chromatin across the genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

28 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Nucleosome and transcription activator antagonism at human beta-globin locus control region DNase I hypersensitive sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome

28 July 2018

1 reference

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A chromatin landmark and transcription initiation at most promoters in human cells

28 July 2018

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

28 July 2018

1 reference

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STAMP: a web tool for exploring DNA-binding motif similarities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Distant regulatory elements in a Sox10-beta GEO BAC transgene are required for expression of Sox10 in the enteric nervous system and other neural crest-derived tissues.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Interchromosomal associations between alternatively expressed loci

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The human genome browser at UCSC

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

A distant upstream promoter of the HNF-4alpha gene connects the transcription factors involved in maturity-onset diabetes of the young

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

IRF family of transcription factors as regulators of host defense

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Functional AP1 and CRE response elements in the human keratinocyte transglutaminase promoter mediating Whn suppression

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The protein CTCF is required for the enhancer blocking activity of vertebrate insulators

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The orphan receptors COUP-TF and HNF-4 serve as accessory factors required for induction of phosphoenolpyruvate carboxykinase gene transcription by glucocorticoids

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Nuclease hypersensitive sites in chromatin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Role of redox signaling regulation in propyl gallate-induced apoptosis of human leukemia cells

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

A map of open chromatin in human pancreatic islets

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping short DNA sequencing reads and calling variants using mapping quality scores

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

29 October 2018

GATA1-related leukaemias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Foxs and Ets in the transcriptional regulation of endothelial cell differentiation and angiogenesis

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202292

29 October 2018

Identifiers

DOI

10.1101/GR.121541.111

1 reference

30 July 2017

1 reference

30 July 2017

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