DATA

Data repositories for our publications

Please also see supplementary materials in the papers themselves.

  1. Data from the CHiCAGO paper (Cairns et al., Genome Biology 2016): https://osf.io/nemc6/.

    HindIII PCHi-C design files for the human and mouse genomes
    Reanalysis of PCHi-C data for GM12878 LCLs (from Mifsud et al., Nat Genet 2015) and mouse ES cells (from Schoenfelder et al., Genome Res 2015)

  2. Data from the GWAS-PCHiC integration paper (Javierre et al., Cell 2016): https://osf.io/u8tzp/.
    Capture design files for the forward and reverse capture
    CHiCAGO objects for PCHi-C data in each of the 17 human primary cell types
    Lists of detected interactions across cell types (“peak matrices”)
    Chromatin annotation of the detected promoter-interacting regions
    Gene expression data
    TAD calls
    GWAS integration data

  3. Data from the PCHi-C analysis of hESC-to-neural differentiation (Freire-Pritchett et al., eLife 2017): https://osf.io/sdbg4/.
    CHiCAGO objects for PCHi-C data in each of the two analysed cell types
    Chromatin annotation of the detected promoter-interacting regions
     Gene expression data
    TAD calls

  4. Data from the Chicdiff paper (Cairns et al., Bioinformatics 2019): https://osf.io/y9nb5/.
    A use example for the Chicdiff pipeline

  5. Data from the promoter-connected TFBS variation paper (Mitchelmore et al., NAR 2020): https://osf.io/fa4u7/.
    List of TF binding affinity CRM variants
    Association data between TF binding affinity CRM variants and gene expression

  6. Data from the PCHi-C analysis of cohesin- and CTCF-depleted cells (Thiecke et al., Cell Reports 2020): https://osf.io/brzuc/.
    CHiCAGO objects for each PCHi-C dataset
    Chicdiff analysis results
    TAD calls
    RNA-seq and SLAM-seq data

  7. PCHi-C-based gene prioritisation of COVID-19 GWAS: https://osf.io/k2mxe/.
    List of prioritised genes
    Manhattan plots and other visualisations