Ontology highlight
ABSTRACT:
PROVIDER: PRJNA980293 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes. The processed heatmap data, showing the number of read pairs corresponding to particular locus pairs in the genome, are linked to the Series record below. The processed eigenvector data used to generate the heatmaps are linked to the Series record below. Additional DNAseI and ChIP-Seq data tracks were used in the paper, and are available at the UCSC browser (http://genome.ucsc.edu/) DNAseI: wgEncodeUwDnaseSeqRawSignalRep2K562 wgEncodeUwDnaseSeqRawSignalRep2Gm06990 ChIP-Seq: wgEncodeBroadChipSeqSignalGm12878H3k36me3 wgEncodeBroadChipSeqSignalGm12878H3k27me3 Interaction maps in 2 different cell types.
2009-10-09 | E-GEOD-18199 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare AR binding activity in LNCaP cells with and without knockdown of GATA2. Methods: LNCaP cells between passage number 32-34 were used for assay. Cells are transfected with GATA2 specific or nonspecific siRNA and ChIP was performed, the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks. Results: GATA2 knockdown lead to changes of AR binding activity , in most AR binding sites, AR shows decreased bindig activity. Only small percent sites show increased binding. Conclusions: Our study represents the first detailed analysis of the relationship between GATA2 and AR binding in whole genomic DNA.These results demostrate GATA2 play a critical role in AR activity in prostate cancer. LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.
2014-01-21 | E-GEOD-52725 | biostudies-arrayexpress
Project description:Millions of cis-regulatory sequences have recently been found in the human genome, but the function of most cis-elements are not yet clear, in part due to the difficulty in determining their regulatory targets, which are often located millions of base pairs away and separated by one or more unrelated genes. To address this problem, the Hi-C method has been developed to identify long-range looping interactions in a genome-wide, unbiased fashion. However, current data analysis of Hi-C datasets cannot fully resolve regulatory interactions between enhancers and promoters due to the low resolution. Here, we generated a high-depth Hi-C dataset and applied a new analysis method that offers improved resolution permitting genome-wide identification of nearly one million chromatin interactions. We demonstrated the use of Hi-C to identify target promoters of enhancers regulated by NF-M-NM-:B signaling and signal-dependent dynamic chromatin interaction at these enhancers in human cells. Surprisingly, our results showed that most NF-M-NM-:B binding sites are looped to their regulatory targets prior to activation of the signaling pathway, and appear to undergo little change during signaling. This observation suggests that the chromatin organization landscape, once established in a cell type, is rather stable and may influence the selection and activation of target genes by a transcription factor. We performed Hi-C analysis using a human fibroblast cell line IMR90 before and after NF-M-NM-:B activation. In the meantime, we also performed ChIP-seq experiments to map the location of NF-M-NM-:B p65 subunit, RNA polymerase II, p300, and several histone modifications (including H3K4me1, H3K4me3, H3K27ac and H3K36me3) in IMR90 cells before and after transient TNF-M-NM-1 stimulation. Additionally, to monitor the dynamic transcription profiles, we also performed Global Run-On sequencing (GRO-seq).
2013-10-20 | E-GEOD-43070 | biostudies-arrayexpress
Project description:Chanodichthys erythropterus Hi-C sequencing data
| PRJNA825086 | ENA
Project description:The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of cell identity genes and repression of genes encoding lineage-specifying developmental regulators. Here we use large ESC cohesin ChIA-PET datasets and other genomic data to identify the local chromosomal structures at both active and repressed genes across the genome. The results show that super-enhancer driven cell identity genes generally occur within large loops that are connected through CTCF-CTCF interaction sites occupied by cohesin. H3K27me3 ChIP-seq data from wild type murine embryonic stem cells V6.5 were generated by deep sequencing using Illumina Hi-Seq 2000.
2014-06-27 | E-GEOD-57912 | biostudies-arrayexpress
Project description:Large scale study on human fibroblast, IMR90, by top-down proteomics on a benchtop Orbitrap QExactive HF instrument. RAW files were collected in three main modes: (i) data-dependent top-2 with high resolution for both MS1 and MS2, or hi/hi; (ii) in hi/hi using the in-house written instrument control software AUTOPILOT; (iii) in med/hi mode, where MS1 scans are acquired with short transients.
2016-07-15 | MSV000079913 | MassIVE
Project description:This SuperSeries is composed of the following subset Series: GSE41541: Expression data from mouse proximal intestinal epithelial Lgr5(hi) stem cells and differentiated villus cells (enterocytes from Atoh1 conditional knockout) GSE41542: H3K79me2 ChIP-seq in mouse proximal intestinal Lgr5(hi) stem cells and villus cells GSE41710: Global gene expression analysis of Dot1l-deficient and control intestinal villus cells in mouse Refer to individual Series
2012-10-13 | E-GEOD-41543 | biostudies-arrayexpress