Transcriptomics

Dataset Information

310

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


ABSTRACT: 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.

ORGANISM(S): Musculus  

SUBMITTER: Daniel Zerbino   Peter Fraser  Cameron Osborne  Andrew Dimond  Paula Freire-Pritchett  Jonathan Cairns  Biola-Maria Javierre  Vincent Plagnol  Steven William Wingett  Csilla Várnai  Mikhail Spivakov  Stefan Schoenfelder  Steven W Wingett 

PROVIDER: E-GEOD-81503 | ArrayExpress | 2016-05-18

SECONDARY ACCESSION(S): SRP075259GSE81503PRJNA321822

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

HiCUP: pipeline for mapping and processing Hi-C data.

Wingett Steven S   Ewels Philip P   Furlan-Magaril Mayra M   Nagano Takashi T   Schoenfelder Stefan S   Fraser Peter P   Andrews Simon S  

F1000Research 20151120


HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and h  ...[more]

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