Dixon 2012, topological domains in human and mouse.


Topologocally associated domains (TADs) and domain boundaries inferred from Hi-C data with the DI (Directionality Index) method. The series contains TAD annotation files for human embryonic stem cells (hESC), mouse embryonic stem cells, human IMR90 cells derived from lung fibroblasts and mouse cortex. Domains are represented by start and end positions, domain boundaries by a single postion corresponding to the center of the range indicated in the source files.



From H. sapiens (March 2006 NCBI36/hg18).

Genome Annotation:

Filename Description Feature GEO-ID
1 dixon12_domains_hESC_rep1.sga hESC|TAD domains||rep1 TAD_domain
2 dixon12_domains_hESC_rep2.sga hESC|TAD domains||rep2 TAD_domain
3 dixon12_domains_hESC_combined.sga hESC|TAD domains||combined TAD_domain
4 dixon12_domains_IMR90_rep1.sga IMR90|TAD domains||rep1 TAD_domain
5 dixon12_domains_IMR90_rep2.sga IMR90|TAD domains||rep2 TAD_domain
6 dixon12_domains_IMR90_combined.sga IMR90|TAD domains||combined TAD_domain
7 dixon12_boundaries_hESC_rep1.sga hESC|TAD boundaries||rep1 TAD_boundary
8 dixon12_boundaries_hESC_rep2.sga hESC|TAD boundaries||rep2 TAD_boundary
9 dixon12_boundaries_hESC_combined.sga hESC|TAD boundaries||combined TAD_boundary
10 dixon12_boundaries_IMR90_rep1.sga IMR90|TAD boundaries||rep1 TAD_boundary
11 dixon12_boundaries_IMR90_rep2.sga IMR90|TAD boundaries||rep2 TAD_boundary
12 dixon12_boundaries_IMR90_combined.sga IMR90|TAD boundaries||combined TAD_boundary

Technical Notes

Excel files were inspected by eye. In one sheet, a backslash in line 1 was manually replaced by "chr1". Individual sheets were exported manually from the two xls files in tab-delimited text format. Carriage return characters where replaced by line feeds. The resulting files conform to BED3 format and were converted into SGA format with bed2sga (ChIP-Seq v1.5.6), using option -r (regional) for TAD domains and option -c (centered) for TAD boundaries. FPS file were generated from SGA files using sga2fps (ChIP-Seq v1.5.5).