Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA230803 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1044392.fastq.gz | Fastqsanger.gz | |||
| SRR1044393.fastq.gz | Fastqsanger.gz | |||
| SRR1044394.fastq.gz | Fastqsanger.gz | |||
| SRR1044395.fastq.gz | Fastqsanger.gz | |||
| SRR1044396.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
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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
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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
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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.
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Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Terry Furey mailto:tsfurey@duke.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks display DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets. DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI "hypersensitivity" is a feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions, and novel elements. DNaseI hypersensitivity signifies chromatin accessibility following binding of trans-acting factors in place of a canonical nucleosome. Together with FAIRE and ChIP-seq experiments, these tracks display the locations of active regulatory elements identified as open chromatin in multiple cell types (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) from the Duke, UNC-Chapel Hill, UT-Austin, and EBI ENCODE group. Within this project, open chromatin was identified using two independent and complementary methods: these DNaseI HS assays and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), combined with chromatin immunoprecipitation (ChIP) for select regulatory factors. DNaseI HS and FAIRE provide assay cross-validation with commonly identified regions delineating the highest confidence areas of open chromatin. ChIP assays provide functional validation and preliminary annotation of a subset of open chromatin sites. Each method employed Illumina (formerly Solexa) sequencing by synthesis as the detection platform. The Tier 1 and Tier 2 cell types were additional verified by a second platform, high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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Project description:Changes in DNaseI hypersensitivity upon co-treatment of cells with Dex and E2
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Project description:Using DNaseI hypersensitivity (HS) assays (Dnase-seq), high resolution DNaseI digestion profiles were generated genome-wide in diverse human cell types. We showed that within general regions of DNaseI HS that are known to identify locations of gene regulatory elements, DNaseI digestion patterns allowed us to identify locations of individual transcription factor binding sites that protected against the bound DNA against digestion. To measure the accuracy of these footprints, we also generated ChIP-seq data for the CTCF DNA binding factor in the same cell growths. We found that DNaseI footprints containing the CTCF canonical binding motif show significant ChIP-seq signal while CTCF binding motifs not in footprints show almost no signal providing one measure of valdation of the DNaseI footprints. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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