Hi-C
Capture Hi C identifies a novel causal gene, IL20RA, in the pan autoimmune genetic susceptibility region 6q23
... Validation of interactions was carried out on biological replicate 3C libraries for each of the cell lines (GM12878 and Jurkat). Libraries were prepared using the cross- linking, digestion with HindIII and ligation steps ...
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HSA: integrating multi track Hi C data for genome scale reconstruction of 3D chromatin structure
... to Hi-C data sets of diverse cell types from humans and ...situ Hi-C data reveals striking consistency across different human cell types, which suggests there are certain invariant 3D ...
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bin3C: exploiting Hi C sequencing data to accurately resolve metagenome assembled genomes
... The real microbiome we analyzed with bin3C was first described in a previous study to demonstrate a metagenomic Hi-C analysis service called ProxiMeta [31]. ProxiMeta is the only other complete solution for ...
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Hi C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours
... from Hi-C and sWGS data were compared to determine their concord- ...between Hi-C and sWGS output values was determined for each bin and the total difference ...
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ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi C
... in Hi-C, employs a very simplistic binomial test coupled with multiple test- ing correction to search for overrepresented interactions, but does not explicitly take into account known features of ...
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Canonical and single cell Hi C reveal distinct chromatin interaction sub networks of mammalian transcription factors
... Although Hi-C quantifies how often two genome regions are in close proximity, light microscopy shows that the spatial distance between loci varies greatly from cell to cell ...canonical Hi-C, ...
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Comparison of the three dimensional organization of sperm and fibroblast genomes using the Hi C approach
... A previous study showed that contact heatmaps could be decomposed into a set of eigenvector tracks. The first eigenvector (E1) values correlate with different genome properties such as replication time, GC content and ...
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Chrom3D: three dimensional genome modeling from Hi C and nuclear lamin genome contacts
... from Hi-C data Interactions between beads were defined from high- resolution Hi-C data for HeLa cells [38] accessed under dbGap number ...
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An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data
... that Hi-C data are drawn from a popula- tion of cells, each with its own independent and unique 3-D ...like Hi-C data at large, this dataset contains a number of biases: the fact that it is ...
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Reconstructing A/B compartments as revealed by Hi C using long range correlations in epigenetic data
... corresponding Hi-C data from a different source ...existing Hi-C data on the mESC line J1 [3] ...have Hi-C data available for this cell type, but based on these observations we ...
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GrapHi C: graph based visualization of Hi C datasets
... To demonstrate the value of the GrapHi-C visualization protocol, it was utilized to visualize contact maps from existing fission yeast datasets where (1) fission yeast mutants were studied to determine principles ...
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CHiCAGO: robust detection of DNA looping interactions in Capture Hi C data
... in Hi-C data is that we expect the fractions of true positives to vary de- pending on the genomic distance between the fragments; in fact, the majority of tests are performed with interac- tions spanning ...
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Determination of the 3D genome organization of bacteria using Hi-C
... 3]. Hi-C is possibly the most powerful of the 3C-based methods as it allows the interrogation of all possible interactions across the genome in an unbiased manner at a resolu- tion of up to 5 kb ...
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Measuring the reproducibility and quality of Hi C data
... of Hi-C data Four recently developed methods for measuring the quality of and reproducibility of Hi-C experiments were assessed in this study ...of Hi-C ...the Hi-C ...
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Software tools for visualizing Hi C data
... by Hi-C ...of Hi-C contacts in the heat map visualization [28] (indicated by the red ...visualized. c A putative promoter–enhancer interaction around the NANOG gene is displayed as a ...
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HiC Pro: an optimized and flexible pipeline for Hi C data processing
... Each aligned read can be assigned to one restriction fragment according to the reference genome and the se- lected restriction enzyme. Both reads are expected to map near a restriction site, and with a distance within ...
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Comparison of Hi C results using in solution versus in nucleus ligation
... solution Hi-C ligation produces a significant amount of random ligation between cross-linked ...ligation Hi- C, a substantial number of un-measurable spurious di- tags from different cells of ...
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Capture Hi-C identifies putative target genes at 33 breast cancer risk loci.
... 32 Where TSS for two or more target genes map to a single HindIII fragment, the genes are separated by a comma. Non-coding RNAs (long non-coding RNAs, microRNAs and small nucleolar RNAs) are indicated in green. There ...
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Identification of recurrent noncoding mutations in B-cell lymphoma using capture Hi-C.
... Figure 4: Copy number variation at cis-regulatory element is associated with CD69 expression in DLBCL. (A) Loss of a CRE interacting with the CD69 promoter. Top panel shows position of CNVs at CRE, all of which are copy ...
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Modeling Of Tow Wrinkling In Automated Fiber Placement Based On Geometrical Considerations
... The BACH employs Markov chain Monte Carlo (MCMC) to maximize the proba- bility and obtain the 3D structure. The process optimizes 3D structure and nuisance parameters iteratively. To compare the performance between the ...
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