High depth genome wide chromatin contact matrix

These high-depth meta-Hi-C chromatin contact matrices are surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, eQTLs, and cross-species relationships. 
For building the meta-Hi-C matrix, we uniformly processed 3619, 6732, and 487 Hi-C runs for Human, Mouse, and Fly respectively. The runs were obtained after querying Sequence Read Archive with field limitations of given species and Hi-C as experiment strategy.  A genome-wide chromatin contact matrix was created for each run after mapping the reads to the same reference genome for each species. Reads were aligned to the hg38, mm10, and dm6 genomes in Human, Mouse and Fly respectively. All chromatin contact matrices for a species were aggregated to create the meta-Hi-C matrix. 
The genome-wide Hi-C matrices were divided into cis (intrachromsomal) and trans (interchromosomal). In cis, each chromosome is stored in a seperate matrix. In trans,  the matrix is genome-wide but with no cis contacts (cis contacts are always 0 in this case). Here the cis contact matrices are available at 10KB and 1KB resolution for all three species. The trans contact matrices are available at 10KB resolution for all three species and additionally at 1KB resolution for Fly. The matrices are stored as *.h5 in HiCMatrix format (https://github.com/deeptools/HiCMatrix). HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/) can be used to process these files or to convert them to other formats if desired. 
Meta-Hi-C matrices at several other resolutions are available for download via online tool at https://gillisweb.cshl.edu/HiC/ or direct download at https://labshare.cshl.edu/shares/gillislab/resource/HiC/

本数据集包含高深度元Hi-C（meta-Hi-C）染色质接触矩阵，其在捕获染色质互作的远程功能关联方面性能优异，当前可用于预测共表达、表达数量性状位点（expression Quantitative Trait Loci, eQTL）以及跨物种关联。
在构建元Hi-C矩阵时，我们统一处理了分别对应人类、小鼠和果蝇的3619、6732及487组Hi-C测序run。这些数据均通过以指定物种和Hi-C为实验策略的字段限定条件，从序列读取档案（Sequence Read Archive, SRA）中检索得到。针对每组测序数据，将测序读段比对至对应物种的参考基因组后，即可生成全基因组染色质接触矩阵：人类、小鼠和果蝇的测序读段分别比对至hg38、mm10及dm6参考基因组。将某一物种的所有染色质接触矩阵进行聚合，即可得到该物种的元Hi-C矩阵。
全基因组Hi-C矩阵可分为顺式（染色体内，intrachromosomal）和反式（染色体间，interchromosomal）两类。顺式矩阵按每条染色体单独存储；反式矩阵为全基因组范围，但不含顺式互作（此时顺式接触值恒为0）。针对三个物种，均提供分辨率为10KB和1KB的顺式接触矩阵；反式接触矩阵则均提供10KB分辨率的版本，其中果蝇额外提供1KB分辨率的版本。所有矩阵均以HiCMatrix格式的*.h5文件存储（详见https://github.com/deeptools/HiCMatrix）。若有需要，可使用HiCExplorer工具（https://hicexplorer.readthedocs.io/en/latest/）对这些文件进行处理或格式转换。
其他多种分辨率的元Hi-C矩阵可通过https://gillisweb.cshl.edu/HiC/提供的在线工具下载，或直接从https://labshare.cshl.edu/shares/gillislab/resource/HiC/获取。