Data processed using the Yaffe-Tanay's normalization approach

The results stored into zip files include:
  • Intra-chromosomal contact matrices (40 kb)
  • Directionality Index
  • HMM states
  • Topological domain coordinates
  • HDF5 files

HDF5 files can be used to obtain quickly contact matrices at a different resolution, directly starting from section 2 of Yaffe-Tanay's data normalization.

For more information about how the data were processed and can be loaded, please see the HiCtool documentation.
Data processed to be used for the matrix balancing normalization approach

Currently, there are no contact data stored here following this normalization method. However, the HiC_project_object.hdf5 file included under the HDF5 files below can be used to generate the observed data to be normalized directly starting from section 2 of matrix balancing data normalization, avoiding all the pre-processing steps.
If you use this data in your research, please cite the manuscript:
​Calandrelli, R., Wu, Q., Guan, J., & Zhong, S. (2018). GITAR: An open source tool for analysis and visualization of Hi-C data. Genomics, proteomics & bioinformatics.
​Homo Sapiens (hg38)
GEO accession number Cell line Reference Contact matrices Directionality index HMM states Topological domains HDF5 files
GSM1909121 Haploid fibroblast-like Hap1 Sanborn et al. (2015)
GSM1718021 Human Embryonic Stem Cells H9 Nagano et al. (2015)
GSM1608505 Lymphoblastoid GM12878 Grubert et al. (2015)
GSM1267200 H1 Mesenchymal stem cells Dixon et al. (2015)
GSM1267196 Embryonic stem cells H1 Dixon et al. (2015)
GSM1551599 Lung Fibroblasts IMR90 (CCL-186) Rao et al. (2014)
GSM1551629 HUVEC (CC-2517) Rao et al. (2014)
GSM1551550 B-lymphoblastoids GM12878 Rao et al. (2014)
GSM1294039 Breast cancer cell line T47D-MTVL, progestin R5020-stimulated Le Dily et al. (2014)
GSM1294038 Breast cancer cell line T47D-MTVL, unstimulated Le Dily et al. (2014)
GSM1081530 HEK293T Zuin et al. (2014)
GSM1906334 MHH-CALL- 4 B-cell acute lymphocytic leukemia CALL4 Wang et al. (2013)
GSM1906333 Primary TumorB-cell acute lymphocytic leukemia B-ALL Wang et al. (2013)
GSM1906332 B-cell Follicular Lymphoma RL Wang et al. (2013)
GSM1055805 Embryonic stem cells H1 Jin et al. (2013)
GSM1055800 Fetal lung fibroblast IMR90 Jin et al. (2013)
GSM927075 ERG prostate epithelial cell line RWPE-1 Rickman et al. (2012)
GSM862724 Fetal lung fibroblast IMR90 Dixon et al. (2012)
GSM862723 Human Embryonic Stem Cells H1 Dixon et al. (2012)
GSM455133 EBV-transformed lymphoblastoid GM06990 Lieberman-Aiden et al. (2009)
Mus Musculus (mm10)
GEO accession number Cell line Reference Contact matrices Directionality index HMM states Topological domains HDF5 files
GSM1551633 B-lymphoblasts CH12-LX Rao et al. (2014)
GSM862720 Mouse Embryonic Stem Cells J1 Dixon et al. (2012)