It is not arduous to acquire the chromatin interactions of interests in the search page. Furthermore, we provide complete interaction datasets in download page, facilitating comprehensive analysis based on massive data. For convenience, genome annotation files, enhancer position files and dbSNPs in different versions of different species are offered as well.


Part 1-1: Interaction pairs with annotation (hg38 and mm10)

File Method Species Cell Type Enhancer Antibody Resolution Geo

Part 1-2: Interaction pairs without annotation (hg38 and mm10)

3c-1.step 4c-1.step 4c-2.step 4c-3.step 4c-4.step 4c-5.step
4c-6.step 4c-7.step 4c-8.step 4c-9.step 5c-1.step 5c-10.step
5c-11.step 5c-12.step 5c-13.step 5c-14.step 5c-15.step 5c-16.step
5c-17.step 5c-18.step 5c-19.step 5c-2.step 5c-20.step 5c-21.step
5c-22.step 5c-23.step 5c-24.step 5c-25.step 5c-26.step 5c-3.step
5c-4.step 5c-5.step 5c-6.step 5c-7.step 5c-8.step 5c-9.step
chia-1.step chia-10.step chia-11.step chia-12.step chia-13.step chia-14.step
chia-15.step chia-16.step chia-2.step chia-3.step chia-4.step chia-5.step
chia-6.step chia-7.step chia-8.step chia-9.step hic-1.step hic-10.step
hic-11.step hic-12.step hic-13.step hic-14.step hic-15.step hic-16.step
hic-17.step hic-18.step hic-19.step hic-2.step hic-20.step hic-21.step
hic-22.step hic-23.step hic-24.step hic-25.step hic-26.step hic-27.step
hic-28.step hic-29.step hic-3.step hic-30.step hic-31.step hic-32.step
hic-33.step hic-34.step hic-35.step hic-36.step hic-37.step hic-38.step
hic-39.step hic-4.step hic-5.step hic-6.step hic-7.step hic-8.step
hic-9.step          

Part 2: Genome annotation file, enhancer positions and SNPs of human and mouse's many cell lines that CCSI database involves can be downloaded as follows:

1. Genome annotation file list

fission yeast.gtf fission yeast.tss hg38.gtf hg38.tss mm10.gtf mm10.tss
readme.txt saccer2.gtf saccer2.tss      

2. Enhancer file list

GM12878.hg38.enhancer Hct116.hg38.enhancer HelaS3.hg38.enhancer Hepg2.hg38.enhancer
IMR90.hg38.enhancer K562.hg38.enhancer MEF.mm10.enhancer Mcf7.hg38.enhancer
cortex.mm10.enhancer hESC.hg38.enhancer limb.mm10.enhancer mESC.mm10.enhancer
mNPC.mm10.enhancer readme.txt    

3. SNP list

hg38-db141 mm10-db137        

Part 3: Analysis pipeline for annotating genes, regulatory regions and SNPs in chromatin interaction pairs was deposited in github: https://github.com/xiexiaowei/CCSI