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