Site-specific silencing of regulatory elements as a mechanism of X-inactivation
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE39406 | GEO | 2012/11/21
SECONDARY ACCESSION(S): PRJNA170844
REPOSITORIES: GEO
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2012-11-21 | E-GEOD-39406 | biostudies-arrayexpress
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Project description:This Series reports data from a CTCF ChIP-Seq experiment performed in F1-hybrid mouse trophoblast stem cells (TSCs). The data are part of a larger study examining inactive X gene expression and chromatin states, reported as GEO Series GSE39406. Included for this dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads Single CTCF ChIP-Seq experiment
2012-09-08 | E-GEOD-40667 | biostudies-arrayexpress
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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 Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) evidence as part of the four Open Chromatin track sets. FAIRE is a method to isolate and identify nucleosome-depleted regions of the genome. FAIRE was initially discovered in yeast and subsequently shown to identify active regulatory elements in human cells (Giresi et al., 2007). Similar to DNaseI HS, FAIRE appears to identify functional regulatory elements that include promoters, enhancers, silencers, insulators, locus control regions and novel elements. Together with DNaseI HS 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: DNaseI hypersensitivity (HS) and these FAIRE assays, 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 additionally verified by a second platform, high-resolution 1% ENCODE tiled microarrays supplied by NimbleGen. Release 1 (March 2011) of this track consists of a remapping of all previously released experiments to the human reference genome GRCh37/hg19 (these data were previously mapped to NCBI36/hg18; please see the Release Notes section of the hg18 Open Chromatin track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeChromatinMap) for information on the NCBI36/hg18 releases of the data). -There are 12 new FAIRE experiments in this release, on 10 new cell lines. -New to this release is a reconfiguration of how this track is displayed in relation to other tracks from the Duke/UNC/UT-Austin/EBI group. -A synthesis of open chromatin evidence from the three assay types was compiled for Tier 1 and 2 cell lines plus NHEK will also be added in this release and can be previewed in: Open Chromatin Synthesis (http://genome-preview.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeOpenChromSynth). -Enhancer and Insulator Functional assays: A subset of DNase and FAIRE regions were cloned into functional tissue culture reporter assays to test for enhancer and insulator activity. 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