Bipartite structure of the inactive mouse X chromosome

Xinxian Deng, Wenxiu Ma, Vijay Ramani, Andrew Hill, Fan Yang, Ferhat Ay, Joel B Berletch, Carl Anthony Blau, Jay Shendure, Zhijun Duan, William S Noble, Christine M Disteche

Genome Biology 16(1):152, 2015

Raw sequencing data

GSE# 68992

Mapped and cleaned sequencing data

The gzipped L1.gz files contain 11 columns. Each row is for a mapped read pair. The columns are read-id, read1-strand, read1-chr, read1-pos, read1-allele, read1-seq, read2-strand, read2-chr, read2-pos, read2-allele, read2-seq. The ref allele is BL6; the alt allele is patski; and the both-ref allele is for ambiguous read.

experiment cell biological replicate raw sequencing
DNase-Hi-C brain rep1 L1.gz
insitu-DNase-Hi-C brain rep1 L1.gz
insitu-DNase-Hi-C patski rep1 L1.gz
insitu-DNase-Hi-C patski rep2 L1.gz

Inferred 3D structures

We first obtained the structures at 1 Mb resolution using PASTIS. Then we refined the resolution using quadratic Bezier curve fitting. The following files are the resulting structures at 10Kb resolution:

In these files,

The pseudo-Spretus genome was built by substituting known SNPs (from the Sanger Institute) into the Black6/mm9 reference genome.