Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tissue/Cell DNaseI sensitivity/hypersensitivity screening II

ABSTRACT: DNaseI hypersensitivity using DNase-array method on Affy platform overall design Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197 This study is part of an ongoing screening process designed to obtain high quality cell-lines/tissues for further high throughput sequencing analysis. Bed files based on hg17 genome build Keywords: genomic

ORGANISM(S): Homo sapiens

PROVIDER: GSE11298 | GEO | 2008/04/30

SECONDARY ACCESSION(S): PRJNA106719

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tissue/Cell DNaseI sensitivity/hypersensitivity screening

Project description:DNaseI hypersensitivity using DNase-array method on Affy platform overall design Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197 Keywords: genomic

2007-09-30 | GSE8962 | GEO

DNaseI sensitivity/hypersensitivity Part II

Project description:DNaseI sensitivity/hypersensitivity using DNase-array method (Sabo et al Nature Methods 3:511-18, 2006) on Affymetrix whole-genome tiling DNA microarrays. Background: Focal alteration in chromatin structure in vivo, detectable through hypersensitivity to DNaseI and other nucleases, is the sine qua non of diverse transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions. Keywords: genomic

2007-06-23 | GSE7411 | GEO

DNaseI sensitivity/hypersensitivity Part I

2007-06-23 | GSE7168 | GEO

DNaseI sensitivity/hypersensitivity

Project description:DNaseI sensitivity/hypersensitivity

| PRJNA101147 | ENA

Genome-wide map of DNaseI hypersensitivity in mouse erythroid cells.

Project description:We generated genome-wide maps of DNaseI hypersensitivity in mouse erythroid cells by DNase-Seq.

2012-01-30 | GSE27919 | GEO

Genome-wide map of DNaseI hypersensitivity in mouse erythroid cells.

Project description:We generated genome-wide maps of DNaseI hypersensitivity in mouse erythroid cells by DNase-Seq. Examination of DNaseI hypersensitivity in mouse erythroid cells.

2012-01-30 | E-GEOD-27919 | biostudies-arrayexpress

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington

Project description:This track is produced as part of the mouse ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in mouse tissues and cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promotors, locus control regions and novel elements. For each experiment (tissue/cell type) this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2012-10-03 | GSE37074 | GEO

DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promotors, locus control regions and novel elements. For each experiment (cell type) this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Raw Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks)." For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2011-06-03 | GSE29692 | GEO

DNase hypersensitivity mapping (DNase-chip) using Nimblegen ENCODE arrays in a variety of human cell types

Project description:DNase hypersensitivity using Nimblegen ENCODE arrays (DNase-chip) in primary human trachea epithelia (pHTE), normal human bronchial epithelia (NHBE), Caco2, HT29, human skin fibroblasts, primary human male epididymis. DNase hypersensitivity mapping is used to detect putative regulatory elements of the human genome. We digested chromatin from the above cell types with DNaseI using the DNase-chip protocol devised by Crawford et al. (Nat. Methods, 2006). Briefly, cells are lysed, chromatin is digested with increasing amounts of DNase I, digested ends are blunted in adequetely digested samples, ligated to biotinylated linkers, purified with streptavidin beads, amplified by LM-PCR. As control, randomly sonicated genomic DNA is used. LM-PCR material was labeled and hybridized to hg_17 ENCODE arrays at Nimblegen facility. DNaseI-digested chromatin was hybridized to Nimblegen ENCODE arrays (build hg17). Randomly sonicated genomic DNA was used as control. Three biological replicates on three arrays were performed for Caco2 cells, three replicates were done with skin fibroblasts (two digestions were pooled and hybridized to a single array [Sample: SkinFibro.sample2]), two replicates on two arrays were performed for pHTE, NHBE, and HT29, and a single experiment for primary male epididymis.

2009-10-31 | E-GEOD-18735 | biostudies-arrayexpress

Whole genome DNAse hypersensitivity in human CD4+ T-cells

Project description:Mapping DNaseI hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. We employed whole genome tiled array strategies to identify DNaseI HS sites within human primary CD4+ T cells. Keywords: whole genome tiling array DNAse hypersensitivity from two biologic replicates of CD4+ T-cells were hybridized to a whole-genome tiling array set (38 arrays each) and compared to the input DNA from the same samples.

2007-11-19 | E-GEOD-8486 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data