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 M. musculus (July 2007 NCBI37/mm9).

Genome Annotation:

Filename Description Feature GEO-ID
1 dixon12_domains_mESC_rep1.sga mESC|TAD domains||rep1 TAD_domain
2 dixon12_domains_mESC_rep2.sga mESC|TAD domains||rep2 TAD_domain
3 dixon12_domains_mESC_combined.sga mESC|TAD domains||combined TAD_domain
4 dixon12_domains_mESC_NcoI.sga mESC|TAD domains||NcoI TAD_domain
5 dixon12_domains_cortex_rep1.sga cortex|TAD domains||rep1 TAD_domain
6 dixon12_domains_cortex_rep2.sga cortex|TAD domains||rep2 TAD_domain
7 dixon12_domains_cortex_combined.sga cortex|TAD domains||combined TAD_domain
8 dixon12_boundaries_mESC_rep1.sga mESC|TAD boundaries||rep1 TAD_boundary
9 dixon12_boundaries_mESC_rep2.sga mESC|TAD boundaries||rep2 TAD_boundary
10 dixon12_boundaries_mESC_combined.sga mESC|TAD boundaries||combined TAD_boundary
11 dixon12_boundaries_cortex_rep1.sga cortex|TAD boundaries||rep1 TAD_boundary
12 dixon12_boundaries_cortex_rep2.sga cortex|TAD boundaries||rep2 TAD_boundary
13 dixon12_boundaries_cortex_combined.sga cortex|TAD boundaries||combined TAD_boundary

Notes on samples nomenclature:

"NcoI" in the 4ht field of the sample description means that the sample has been processed with restriction enduclease NcoI. All other samples were processed with HindIII.

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).