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1
ENCODE Regulation DNase HS Track Settings
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeRegDnase
› cgi-bin › hgTrackUi › g=wg...
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https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeRegDnase
› cgi-bin › hgTrackUi › g=wg...
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2
and biological spectrum of human DNase I hypersensitive sites
https://www.nature.com/articles/s41586-020-2559-3
DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA and contain genetic variations associated with diseases and ...
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https://www.nature.com/articles/s41586-020-2559-3
DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA and contain genetic variations associated with diseases and ...
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3
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001046
For DNase hypersensitive sites, we observe a steady increase in the mean number of sites discovered as additional cell types are tested up to ...
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https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001046
For DNase hypersensitive sites, we observe a steady increase in the mean number of sites discovered as additional cell types are tested up to ...
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4
DNase I hypersensitivity analysis of the mouse brain and ...
https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/1756-8935-8-8
Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied ...
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https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/1756-8935-8-8
Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied ...
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5
ENCODE Project at UCSC: Data Release Policy
http://seabass.mpipz.mpg.de/ENCODE/downloads.html
DNase Clusters, Digital DNaseI Hypersensitivity Clusters from ENCODE. Layered H3K27Ac, H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell ...
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http://seabass.mpipz.mpg.de/ENCODE/downloads.html
DNase Clusters, Digital DNaseI Hypersensitivity Clusters from ENCODE. Layered H3K27Ac, H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell ...
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6
DNase-seq Data Standards and Processing Pipeline - encode
https://www.encodeproject.org/data-standards/dnase-seq-encode4/
DNaseI-seq, or DNase-seq as it is referred to on the ENCODE portal, is a global and high-resolution method that uses the non-specific endonuclease DNaseI to ...
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https://www.encodeproject.org/data-standards/dnase-seq-encode4/
DNaseI-seq, or DNase-seq as it is referred to on the ENCODE portal, is a global and high-resolution method that uses the non-specific endonuclease DNaseI to ...
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7
What does our genome encode?
https://genome.cshlp.org/content/22/9/1602.long
Analysis of ENCODE pilot project data revealed a high ratio of mono- to trimethylated H3K4 at a subset of distal DNase I hypersensitive sites (The ENCODE ...
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https://genome.cshlp.org/content/22/9/1602.long
Analysis of ENCODE pilot project data revealed a high ratio of mono- to trimethylated H3K4 at a subset of distal DNase I hypersensitive sites (The ENCODE ...
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8
Atlas of Transcription Factor Binding Sites from ENCODE ...
https://archive.hshsl.umaryland.edu/handle/10713/13681
Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types ; Journal. Cell Reports ; Publisher.
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https://archive.hshsl.umaryland.edu/handle/10713/13681
Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types ; Journal. Cell Reports ; Publisher.
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9
BinDNase: a discriminatory approach for transcription factor ...
https://academic.oup.com/bioinformatics/article/31/17/2852/184037
Recent studies have shown that genome-wide sequencing data on open chromatin sites from a DNase I hypersensitivity experiments (DNase-seq) has a great potential ...
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https://academic.oup.com/bioinformatics/article/31/17/2852/184037
Recent studies have shown that genome-wide sequencing data on open chromatin sites from a DNase I hypersensitivity experiments (DNase-seq) has a great potential ...
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10
Atlas of Transcription Factor Binding Sites from ENCODE ...
https://www.researchgate.net/publication/343733953_Atlas_of_Transcription_Factor_Binding_Sites_from_ENCODE_DNase_Hypersensitivity_Data_across_27_Tissue_Types
ENCODE DNase Hypersensitivity Data across 27. Tissue Types. Graphical Abstract ... functional annotation of the human genome (Encode Project.
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https://www.researchgate.net/publication/343733953_Atlas_of_Transcription_Factor_Binding_Sites_from_ENCODE_DNase_Hypersensitivity_Data_across_27_Tissue_Types
ENCODE DNase Hypersensitivity Data across 27. Tissue Types. Graphical Abstract ... functional annotation of the human genome (Encode Project.
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11
Comparative evaluation of DNase-seq footprint identification ...
https://www.frontiersin.org/articles/10.3389/fgene.2014.00278/full
These regions, called DNase Hypersensitive Sites (DHSs), are available to the binding of transcription factors (TFs) and are therefore ...
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https://www.frontiersin.org/articles/10.3389/fgene.2014.00278/full
These regions, called DNase Hypersensitive Sites (DHSs), are available to the binding of transcription factors (TFs) and are therefore ...
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12
Genome-scale mapping of DNase I sensitivity in vivo using ...
https://noble.gs.washington.edu/papers/sabo_genome.pdf
of minor DNase I hypersensitive sites). This suggests that only a small fraction of transcriptional regulatory information may be encoded ...
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https://noble.gs.washington.edu/papers/sabo_genome.pdf
of minor DNase I hypersensitive sites). This suggests that only a small fraction of transcriptional regulatory information may be encoded ...
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13
Atlas of Transcription Factor Binding Sites from ENCODE DNase ...
https://www.semanticscholar.org/paper/Atlas-of-Transcription-Factor-Binding-Sites-from-27-Funk-Casella/ced8c96e0123950331c8303ebe09c3613f29556a
DNase-seq footprinting provides a means to predict genome-wide binding sites for ... Sites from ENCODE DNase Hypersensitivity Data Across 27 Tissue Types.
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https://www.semanticscholar.org/paper/Atlas-of-Transcription-Factor-Binding-Sites-from-27-Funk-Casella/ced8c96e0123950331c8303ebe09c3613f29556a
DNase-seq footprinting provides a means to predict genome-wide binding sites for ... Sites from ENCODE DNase Hypersensitivity Data Across 27 Tissue Types.
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14
DNase-seq footprinting Tutorial - Chipster
https://chipster.csc.fi/material/chipseq2014/tutorials/jason/Tutorial/
If you are working with ENCODE data, you can get the data pre-aligned in .bam ... You can find Dgf (digital genomic footprinting) reads and hypersensitive ...
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https://chipster.csc.fi/material/chipseq2014/tutorials/jason/Tutorial/
If you are working with ENCODE data, you can get the data pre-aligned in .bam ... You can find Dgf (digital genomic footprinting) reads and hypersensitive ...
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15
E-GEOD-40869 - DNaseI Digital Genomic Footprinting from ...
https://www.omicsdi.org/dataset/arrayexpress-repository/E-GEOD-40869
A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were ...
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https://www.omicsdi.org/dataset/arrayexpress-repository/E-GEOD-40869
A massively parallel next-generation sequencing technique to define the DNase hypersensitive sites in the genome was adopted. The DNase samples were ...
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16
a high-resolution method to identify DNase I hypersensitive ...
https://europepmc.org/article/pmc/pmc2698431
Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including promoters, ...
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https://europepmc.org/article/pmc/pmc2698431
Mapping DNase I hypersensitive sites is an accurate method of identifying the location of gene regulatory elements, including promoters, ...
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17
Defining functional DNA elements in the human genome | PNAS
https://www.pnas.org/content/111/17/6131
The fraction of the human genome covered by ENCODE-detected elements in at least ... DNAse hypersensitivity and transcription-factor (TFBS) and histone-mark ...
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https://www.pnas.org/content/111/17/6131
The fraction of the human genome covered by ENCODE-detected elements in at least ... DNAse hypersensitivity and transcription-factor (TFBS) and histone-mark ...
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18
Thurman 2012, DNaseI Hypersensitivity by Digital DNaseI ...
https://ccg.epfl.ch/mga/hg19/encode/UW-DNaseI-HS/UW-DNaseI-HS.html
› mga › encode › UW-DNaseI-HS
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https://ccg.epfl.ch/mga/hg19/encode/UW-DNaseI-HS/UW-DNaseI-HS.html
› mga › encode › UW-DNaseI-HS
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19
Integrated DNase I hypersensitivity prediction using RNA-seq ...
https://jscholarship.library.jhu.edu/handle/1774.2/61632
We developed an integrated model KNIT, KNN-BIRD DNase I hypersensitivity prediction from transcriptome, to predict DNase-seq data from RNA-seq gene ...
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https://jscholarship.library.jhu.edu/handle/1774.2/61632
We developed an integrated model KNIT, KNN-BIRD DNase I hypersensitivity prediction from transcriptome, to predict DNase-seq data from RNA-seq gene ...
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20
DNase I sensitivity QTLs are a major determinant of human ...
https://web.stanford.edu/group/pritchardlab/publications/pdfs/Degner12.pdf
We call such variants 'DNase I sensitivity quantitative trait loci' (dsQTLs). ... ENCODE Project in one or more lymphoblastoid cell lines10,23.
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https://web.stanford.edu/group/pritchardlab/publications/pdfs/Degner12.pdf
We call such variants 'DNase I sensitivity quantitative trait loci' (dsQTLs). ... ENCODE Project in one or more lymphoblastoid cell lines10,23.
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21
Using DNase I hypersensitivity Data for Transcription Factor ...
https://aaltodoc.aalto.fi/bitstream/handle/123456789/13586/master_K%E4h%E4r%E4_Juhani_2014.pdf?sequence=1
For example, some of the digital DNase I data sets which are available on the ENCODE project page have prepro-.
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https://aaltodoc.aalto.fi/bitstream/handle/123456789/13586/master_K%E4h%E4r%E4_Juhani_2014.pdf?sequence=1
For example, some of the digital DNase I data sets which are available on the ENCODE project page have prepro-.
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22
DNase-seq footprinting Tutorial - PythonHosted.org
https://pythonhosted.org/pyDNase/tutorial.html
If you are working with ENCODE data, you can get the data pre-aligned in .bam ... You can find Dgf (digital genomic footprinting) reads and hypersensitive ...
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https://pythonhosted.org/pyDNase/tutorial.html
If you are working with ENCODE data, you can get the data pre-aligned in .bam ... You can find Dgf (digital genomic footprinting) reads and hypersensitive ...
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23
New insights into the human genome by ENCODE project
https://www.slideshare.net/TNAUgenomics/new-insights-into-the-human-genome-by-encode-project
Protein bound regions • 119 different DNA-binding proteins and a number of RNA polymerase ... DNase I hypersensitive sites and footprinting • ...
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https://www.slideshare.net/TNAUgenomics/new-insights-into-the-human-genome-by-encode-project
Protein bound regions • 119 different DNA-binding proteins and a number of RNA polymerase ... DNase I hypersensitive sites and footprinting • ...
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24
DNase-Seq/DNasel-Seq - Illumina
https://www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/dnase-seq-dnasel-seq.html
DNase l is sequence-specific and hypersensitive sites might not account for the entire genome6; DNA loss through the multiple purification steps limits ...
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https://www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/dnase-seq-dnasel-seq.html
DNase l is sequence-specific and hypersensitive sites might not account for the entire genome6; DNA loss through the multiple purification steps limits ...
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25
Digital genomic footprinting - Jeff Vierstra, Ph.D.
http://vierstra.org/resources/dgf
Genomic DNase I footprinting enables quantitative, ... and thereby the sequence elements that encode transcription factor recognition sites.
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http://vierstra.org/resources/dgf
Genomic DNase I footprinting enables quantitative, ... and thereby the sequence elements that encode transcription factor recognition sites.
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26
DNase I hypersensitive site - Wikipedia
https://en.wikipedia.org/wiki/DNase_I_hypersensitive_site
In genetics, DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the DNase I enzyme. In these specific regions of ...
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https://en.wikipedia.org/wiki/DNase_I_hypersensitive_site
In genetics, DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the DNase I enzyme. In these specific regions of ...
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27
Perspectives on ENCODE - Yeo Lab
https://yeolab.github.io/papers/2020/ENCODE_2020b_Nature.pdf
major ENCODE assays (ChIP–seq, DNase I hypersensitive sites sequenc- ing (DNase-seq), RNA-seq, and whole-genome bisulfite sequenc-.
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https://yeolab.github.io/papers/2020/ENCODE_2020b_Nature.pdf
major ENCODE assays (ChIP–seq, DNase I hypersensitive sites sequenc- ing (DNase-seq), RNA-seq, and whole-genome bisulfite sequenc-.
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28
CRISPR Encodes Movie into Bacteria, Then DNA Sequencing ...
https://www.genengnews.com/topics/genome-editing/crispr-encodes-movie-into-bacteria-then-dna-sequencing-plays-it/
A new CRISPR system-based technology enables the recording of digital data, like those presenting successive frames of the movie of a ...
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https://www.genengnews.com/topics/genome-editing/crispr-encodes-movie-into-bacteria-then-dna-sequencing-plays-it/
A new CRISPR system-based technology enables the recording of digital data, like those presenting successive frames of the movie of a ...
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