Download Hi-C Data!

This page pertains to the data generated by the paper Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-380.

Here you can download various aspects of the data, including the Hi-C interaction matrices for each chromosome, and the positions of the domains identified by our analysis. To download the raw sequencing data and the mapped reads, please visit the GEO Database under the GEO accession number GSE35156

We have interaction matrices for each of the four cell types analysis (mouse ES cell, mouse cortex, human ES cell (H1), and IMR90 fibroblasts). The interaction matrices are created using either a 40kb bin size throughout the genome. Here, you can download both the raw interaction matrices and the normalized matrices (normalized according to the method described by Yaffe and Tanay). Each of the datasets can downloaded here as a tarball containing 40kb raw(uij's) or normalized(nij's=uij/eij) interaction matrices. We only have the intrachromosomal interaction matrices available here.

Mouse ES Cell Raw Matrices(53 Mb)

Mouse ES Cell Normalized Matrices(1.2 Gb)

Mouse Cortex Raw Matrices(45 Mb)

Mouse Cortex Normalized Matrices(1.2 Gb)

Human ES Cell Raw Matrices(45 Mb)

Human ES Cell Normalized Matrices(1.4 Gb)

Human IMR90 Fibroblast Raw Matrices(60 Mb)

Human IMR90 Fibroblast Normalized Matrices(1.5 Gb)

We also have the locations of each of the topological domains that we call in the data. The method used for called the topological domains is outlined in our paper. The domains for each dataset are provided as bed files, with each line containing the chromosome, domain start, and domain end. The domains were called using the normalized data with a bin size of 40kb, so each domain start and end will be a multiple of 40000.

Mouse ES cell topological domains (47 Kb)

Mouse Cortex topological domains (26 Kb)

Human ES Cell (H1) topological domains (47 Kb)

Human IMR90 Fibroblast topological domains (39 Kb)

The pipeline to call domains from Hi-C experiments:
Hi-C Domain Caller