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.

• Processed data was downloaded from: https://www.nature.com/articles/nature11082 (Supplementary Tables 3 and 4)
• Input file format: XLS
• Download date: 17-4-2020

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.

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).

• Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B
  Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082. 22495300