Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

ABSTRACT: CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

PROVIDER: PRJNA321822 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

Project description:Capture Hi-C (CHi-C) is a state-of-the art method for profiling chromosomal interactions involving targeted regions of interest (such as gene promoters) globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model, and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments, in which many spatially dispersed regions are captured, such as in Promoter CHi-C. We implement these procedures in CHiCAGO (http://regulatorygenomicsgroup.org/chicago), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs. Three human CHi-C biological replicates were generated (comprising 1, 2and 3 technical replicates). Two mouse CHi-C biological replicates were generated (both comprising three technical replicates) and a mouse Hi-C dataset. The publicly available HiCUP pipeline (doi: 10.12688/f1000research.7334.1) was used to process the raw sequencing reads. This pipeline was used to map the read pairs against the mouse (mm9) and human (hg19) genomes, to filter experimental artefacts (such as circularized reads and re-ligations), and to remove duplicate reads. For the CHi-C data, the resulting BAM files were processed into CHiCAGO input files, retaining only those read pairs that mapped, at least on one end, to a captured bait. CHiCAGO then identified Hi-C restriction fragments interacting, with statistical significant, to captured baits.

2016-05-18 | E-GEOD-81503 | biostudies-arrayexpress

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

2016-05-18 | GSE81503 | GEO

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

Project description:Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.

| S-EPMC4908757 | biostudies-literature

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C (4C validation)

Project description:Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks. The results of the analysis on existing mouse ES Capture Hi-C data (ArrayExpress E-MTAB-2414) were validated by two 4C-seq experiments, submitted here.

2019-04-17 | GSE129884 | GEO

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C (4C validation)

Project description:ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C (4C validation)

| PRJNA533097 | ENA

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.

| S-EPMC6532271 | biostudies-literature

A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [Capture Hi-C]

Project description:A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [Capture Hi-C]

| PRJNA508609 | ENA

Hi-CoP, a simple and robust assay for detecting interactions of regulatory regions

Project description:First we developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of accessible regions by directly purifying fragmentized crosslinked chromatin with DNA purification column. The CoP chromatin regions by CoP-seq are consistent with the accessible regions detected by ATAC-seq and FARIE-seq. Then we integrated CoP-seq and Hi-C technique (Hi-CoP) for interactions of accessible chromatin regions which represent active cis-regulatory elements in cells. Our data showed that Hi-CoP assay can robustly detect interactions of regulatory regions.

2020-01-29 | GSE144412 | GEO

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [Hi-C]

Project description:ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry [Hi-C]

| PRJNA991939 | ENA

Hi-C and capture Hi-C for HPV16 infected human W12 cervical cell lines and normal cervical tissue

Project description:Two biological replicates Hi-C and HPV16-specific Region Capture Hi-C libraries were prepared for each of the W12 cell lines. Capture Hi-C was performed using HPV16-specific RNA baits. Hi-C libraries alone were prepared from normal cervix tissue (Ncx).

2021-06-18 | E-MTAB-10152 | 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