- 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)
- 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
- 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
- Data from the Chicdiff paper (Cairns et al., Bioinformatics 2019): https://osf.io/y9nb5/.
- A use example for the Chicdiff pipeline
- 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
- 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
- PCHi-C-based gene prioritisation of COVID-19 GWAS: https://osf.io/k2mxe/.
- List of prioritised genes
- Manhattan plots and other visualisations
