Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of lincRNA genes in human cells

Wenxiu Ma, Ferhat Ay, Choli Lee, Gunhan Gulsoy, Xinxian Deng, Savannah Cook, Jennifer Hesson, Carol B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine Disteche, William S. Noble, ZhiJun Duan

Nature Methods 2015

Raw sequencing data

experiment library cell biological replicate raw sequencing
DNase Hi-C whole-genome H1 rep1 fastq files
DNase Hi-C whole-genome K562 rep1 fastq files
targeted DNase Hi-C P-E H1 rep1 fastq files
targeted DNase Hi-C P-E K562 rep1 fastq files
targeted DNase Hi-C lincRNA-P H1 rep1 fastq files
targeted DNase Hi-C lincRNA-P H1 rep2 fastq files
targeted DNase Hi-C lincRNA-P K562 rep1 fastq files
targeted DNase Hi-C lincRNA-P K562 rep2 fastq files

Interacton Matrix (hg19)

It's in sparse representation. Five columns each line: chr1, midpos1, chr2, midpos2, counts. Filename indicates the matrix resolution.

experiment library cell biological replicate
DNase Hi-C whole-genome H1 rep1 matrix files
DNase Hi-C whole-genome K562 rep1 matrix files
targeted DNase Hi-C P-E H1 rep1 matrix files
targeted DNase Hi-C P-E K562 rep1 matrix files
targeted DNase Hi-C lincRNA-P H1 combined matrix files
targeted DNase Hi-C lincRNA-P K562 combined matrix files

Significant Contact Calls

experiment library cell biological replicate Significant contacting pairs
targeted DNase Hi-C P-E H1 rep1 Supplementary Table 8
targeted DNase Hi-C P-E K562 rep1 Supplementary Table 9
targeted DNase Hi-C lincRNA-P H1 combined Supplementary Table 16
targeted DNase Hi-C lincRNA-P K562 combined Supplementary Table 17

Topological domains (hg19)

experiment library cell biological replicate TADs
DNase Hi-C whole-genome H1 combined bed file
DNase Hi-C whole-genome K562 combined bed file