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

Raw sequencing data

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.

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:

• Brain Spretus allele (inactive X)
• Brain Black6 allele (active X)
• Patski Spretus allele (active X)
• Patski Black6 allele (inactive X)

In these files,

• column #1 is the genomic coordinate of the left edge of each bin,
• columns #2-4 are the x, y, and z coordinates, and
• column #5 is a 0/1 indicator, where 0 means that the genomic region has low mappability and the corresponding row/column in the Hi-C matrix is masked.

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